Multiple sequence alignment - TraesCS4A01G265700

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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 TraesCS4A01G265700 chr4A 100.000 2414 0 0 1 2414 577807872 577805459 0.000000e+00 4458.0
1 TraesCS4A01G265700 chr4A 78.067 652 66 38 478 1078 577853840 577853215 8.270000e-90 340.0
2 TraesCS4A01G265700 chr4A 81.971 416 44 15 735 1142 577866178 577865786 8.320000e-85 324.0
3 TraesCS4A01G265700 chr4A 76.211 702 103 43 471 1144 577847546 577846881 1.800000e-81 313.0
4 TraesCS4A01G265700 chr4A 84.362 243 20 3 1303 1527 577763450 577763208 3.120000e-54 222.0
5 TraesCS4A01G265700 chr4A 95.000 40 2 0 1105 1144 577852964 577852925 2.000000e-06 63.9
6 TraesCS4A01G265700 chr3D 89.669 755 75 3 1556 2309 456139062 456139814 0.000000e+00 959.0
7 TraesCS4A01G265700 chr3B 89.776 714 69 2 1557 2269 137139845 137139135 0.000000e+00 911.0
8 TraesCS4A01G265700 chr3B 100.000 54 0 0 1 54 44291128 44291181 1.530000e-17 100.0
9 TraesCS4A01G265700 chr3B 96.364 55 2 0 1 55 820142253 820142199 9.190000e-15 91.6
10 TraesCS4A01G265700 chr6B 86.508 756 92 10 1558 2309 54219745 54220494 0.000000e+00 822.0
11 TraesCS4A01G265700 chr6B 89.002 591 61 3 1557 2143 669336047 669336637 0.000000e+00 728.0
12 TraesCS4A01G265700 chr2A 89.376 593 58 4 1556 2143 753698733 753698141 0.000000e+00 741.0
13 TraesCS4A01G265700 chr5D 88.702 593 62 4 1556 2143 272361351 272361943 0.000000e+00 719.0
14 TraesCS4A01G265700 chr5D 87.331 592 70 4 1557 2143 506233649 506234240 0.000000e+00 673.0
15 TraesCS4A01G265700 chr5B 88.514 592 63 4 1557 2143 544408064 544408655 0.000000e+00 712.0
16 TraesCS4A01G265700 chr5B 85.795 176 22 2 76 249 520361048 520360874 1.470000e-42 183.0
17 TraesCS4A01G265700 chr1D 86.855 601 74 5 1557 2154 401003769 401003171 0.000000e+00 667.0
18 TraesCS4A01G265700 chr4D 81.199 851 98 32 623 1440 25418901 25419722 1.580000e-176 628.0
19 TraesCS4A01G265700 chr4D 84.858 634 42 16 965 1556 25431293 25431914 7.430000e-165 590.0
20 TraesCS4A01G265700 chr4D 80.614 521 70 18 645 1142 25391323 25391835 8.150000e-100 374.0
21 TraesCS4A01G265700 chr4D 83.028 436 51 17 721 1140 25401343 25401771 8.150000e-100 374.0
22 TraesCS4A01G265700 chr4D 84.890 364 41 5 250 611 25418503 25418854 2.950000e-94 355.0
23 TraesCS4A01G265700 chr4D 81.109 487 44 19 670 1142 25427205 25427657 1.780000e-91 346.0
24 TraesCS4A01G265700 chr4D 88.055 293 34 1 1150 1441 25427710 25428002 1.780000e-91 346.0
25 TraesCS4A01G265700 chr4D 90.991 111 4 1 2307 2411 25431904 25432014 6.960000e-31 145.0
26 TraesCS4A01G265700 chr4B 78.960 846 94 44 630 1428 37410961 37411769 1.290000e-137 499.0
27 TraesCS4A01G265700 chr4B 82.941 510 53 19 645 1142 37403950 37404437 1.710000e-116 429.0
28 TraesCS4A01G265700 chr4B 81.835 556 48 26 401 917 37423824 37424365 3.710000e-113 418.0
29 TraesCS4A01G265700 chr4B 80.408 490 63 13 967 1433 37574680 37574201 2.300000e-90 342.0
30 TraesCS4A01G265700 chr4B 83.278 299 30 13 846 1144 37463894 37464172 8.560000e-65 257.0
31 TraesCS4A01G265700 chr4B 78.759 419 62 24 738 1142 37550427 37550832 3.080000e-64 255.0
32 TraesCS4A01G265700 chr4B 87.065 201 20 5 944 1144 37429179 37429373 3.120000e-54 222.0
33 TraesCS4A01G265700 chr4B 86.000 200 9 7 721 917 37570352 37570169 1.890000e-46 196.0
34 TraesCS4A01G265700 chr4B 93.617 94 5 1 299 391 37572385 37572292 3.240000e-29 139.0
35 TraesCS4A01G265700 chr4B 86.842 114 8 4 715 822 37566691 37566803 1.170000e-23 121.0
36 TraesCS4A01G265700 chr2B 100.000 32 0 0 1 32 717093499 717093530 2.590000e-05 60.2


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 TraesCS4A01G265700 chr4A 577805459 577807872 2413 True 4458.000000 4458 100.00000 1 2414 1 chr4A.!!$R2 2413
1 TraesCS4A01G265700 chr4A 577846881 577847546 665 True 313.000000 313 76.21100 471 1144 1 chr4A.!!$R3 673
2 TraesCS4A01G265700 chr4A 577852925 577853840 915 True 201.950000 340 86.53350 478 1144 2 chr4A.!!$R5 666
3 TraesCS4A01G265700 chr3D 456139062 456139814 752 False 959.000000 959 89.66900 1556 2309 1 chr3D.!!$F1 753
4 TraesCS4A01G265700 chr3B 137139135 137139845 710 True 911.000000 911 89.77600 1557 2269 1 chr3B.!!$R1 712
5 TraesCS4A01G265700 chr6B 54219745 54220494 749 False 822.000000 822 86.50800 1558 2309 1 chr6B.!!$F1 751
6 TraesCS4A01G265700 chr6B 669336047 669336637 590 False 728.000000 728 89.00200 1557 2143 1 chr6B.!!$F2 586
7 TraesCS4A01G265700 chr2A 753698141 753698733 592 True 741.000000 741 89.37600 1556 2143 1 chr2A.!!$R1 587
8 TraesCS4A01G265700 chr5D 272361351 272361943 592 False 719.000000 719 88.70200 1556 2143 1 chr5D.!!$F1 587
9 TraesCS4A01G265700 chr5D 506233649 506234240 591 False 673.000000 673 87.33100 1557 2143 1 chr5D.!!$F2 586
10 TraesCS4A01G265700 chr5B 544408064 544408655 591 False 712.000000 712 88.51400 1557 2143 1 chr5B.!!$F1 586
11 TraesCS4A01G265700 chr1D 401003171 401003769 598 True 667.000000 667 86.85500 1557 2154 1 chr1D.!!$R1 597
12 TraesCS4A01G265700 chr4D 25418503 25419722 1219 False 491.500000 628 83.04450 250 1440 2 chr4D.!!$F3 1190
13 TraesCS4A01G265700 chr4D 25391323 25391835 512 False 374.000000 374 80.61400 645 1142 1 chr4D.!!$F1 497
14 TraesCS4A01G265700 chr4D 25427205 25432014 4809 False 356.750000 590 86.25325 670 2411 4 chr4D.!!$F4 1741
15 TraesCS4A01G265700 chr4B 37410961 37411769 808 False 499.000000 499 78.96000 630 1428 1 chr4B.!!$F2 798
16 TraesCS4A01G265700 chr4B 37423824 37424365 541 False 418.000000 418 81.83500 401 917 1 chr4B.!!$F3 516
17 TraesCS4A01G265700 chr4B 37570169 37574680 4511 True 225.666667 342 86.67500 299 1433 3 chr4B.!!$R1 1134

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
919 8492 0.034337 TTGTCCCTCGCTTGGTACAC 59.966 55.0 0.0 0.0 39.29 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 9677 0.522076 GATTTGCAGCTTCGAAGGCG 60.522 55.0 25.77 14.35 39.35 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
18 19 3.946604 TGCCCTTTATCGTCTGCAA 57.053 47.368 0.00 0.00 0.00 4.08
19 20 2.192664 TGCCCTTTATCGTCTGCAAA 57.807 45.000 0.00 0.00 0.00 3.68
20 21 2.722094 TGCCCTTTATCGTCTGCAAAT 58.278 42.857 0.00 0.00 0.00 2.32
21 22 2.682856 TGCCCTTTATCGTCTGCAAATC 59.317 45.455 0.00 0.00 0.00 2.17
22 23 2.286418 GCCCTTTATCGTCTGCAAATCG 60.286 50.000 0.00 0.00 0.00 3.34
23 24 2.936498 CCCTTTATCGTCTGCAAATCGT 59.064 45.455 0.00 0.00 0.00 3.73
26 27 2.951457 TATCGTCTGCAAATCGTCCA 57.049 45.000 0.00 0.00 0.00 4.02
29 30 0.994995 CGTCTGCAAATCGTCCAGAG 59.005 55.000 0.00 0.00 36.38 3.35
30 31 1.670087 CGTCTGCAAATCGTCCAGAGT 60.670 52.381 0.00 0.00 36.38 3.24
31 32 1.728971 GTCTGCAAATCGTCCAGAGTG 59.271 52.381 0.00 0.00 36.38 3.51
32 33 1.344438 TCTGCAAATCGTCCAGAGTGT 59.656 47.619 0.00 0.00 32.30 3.55
33 34 1.462283 CTGCAAATCGTCCAGAGTGTG 59.538 52.381 0.00 0.00 0.00 3.82
34 35 1.202639 TGCAAATCGTCCAGAGTGTGT 60.203 47.619 0.00 0.00 0.00 3.72
35 36 1.461127 GCAAATCGTCCAGAGTGTGTC 59.539 52.381 0.00 0.00 0.00 3.67
37 38 0.959553 AATCGTCCAGAGTGTGTCGT 59.040 50.000 3.06 0.00 0.00 4.34
38 39 0.959553 ATCGTCCAGAGTGTGTCGTT 59.040 50.000 3.06 0.00 0.00 3.85
39 40 0.742505 TCGTCCAGAGTGTGTCGTTT 59.257 50.000 3.06 0.00 0.00 3.60
40 41 0.852777 CGTCCAGAGTGTGTCGTTTG 59.147 55.000 0.00 0.00 0.00 2.93
41 42 1.801395 CGTCCAGAGTGTGTCGTTTGT 60.801 52.381 0.00 0.00 0.00 2.83
45 46 2.794910 CCAGAGTGTGTCGTTTGTGTAG 59.205 50.000 0.00 0.00 0.00 2.74
46 47 2.218759 CAGAGTGTGTCGTTTGTGTAGC 59.781 50.000 0.00 0.00 0.00 3.58
47 48 2.159156 AGAGTGTGTCGTTTGTGTAGCA 60.159 45.455 0.00 0.00 0.00 3.49
48 49 1.931172 AGTGTGTCGTTTGTGTAGCAC 59.069 47.619 0.00 0.00 34.56 4.40
49 50 1.661617 GTGTGTCGTTTGTGTAGCACA 59.338 47.619 0.00 0.00 43.02 4.57
52 53 1.217882 GTCGTTTGTGTAGCACAGCT 58.782 50.000 2.17 0.00 45.39 4.24
54 55 0.161658 CGTTTGTGTAGCACAGCTCG 59.838 55.000 0.00 5.56 45.39 5.03
55 56 0.512952 GTTTGTGTAGCACAGCTCGG 59.487 55.000 0.00 0.00 45.39 4.63
57 58 2.815647 GTGTAGCACAGCTCGGCC 60.816 66.667 0.00 0.00 40.44 6.13
58 59 2.997315 TGTAGCACAGCTCGGCCT 60.997 61.111 0.00 0.00 40.44 5.19
59 60 2.510238 GTAGCACAGCTCGGCCTG 60.510 66.667 0.00 0.00 40.44 4.85
60 61 2.997315 TAGCACAGCTCGGCCTGT 60.997 61.111 0.00 0.00 46.47 4.00
62 63 1.254975 TAGCACAGCTCGGCCTGTTA 61.255 55.000 0.00 0.00 43.19 2.41
63 64 2.391389 GCACAGCTCGGCCTGTTAC 61.391 63.158 0.00 0.00 43.19 2.50
64 65 1.293498 CACAGCTCGGCCTGTTACT 59.707 57.895 0.00 0.00 43.19 2.24
65 66 1.016130 CACAGCTCGGCCTGTTACTG 61.016 60.000 0.00 3.84 43.19 2.74
66 67 2.103042 CAGCTCGGCCTGTTACTGC 61.103 63.158 0.00 0.00 0.00 4.40
67 68 2.266055 GCTCGGCCTGTTACTGCT 59.734 61.111 0.00 0.00 0.00 4.24
68 69 2.103042 GCTCGGCCTGTTACTGCTG 61.103 63.158 0.00 0.94 35.14 4.41
69 70 2.047274 TCGGCCTGTTACTGCTGC 60.047 61.111 0.00 0.00 33.81 5.25
70 71 3.490759 CGGCCTGTTACTGCTGCG 61.491 66.667 0.00 0.00 0.00 5.18
71 72 3.127533 GGCCTGTTACTGCTGCGG 61.128 66.667 6.98 6.98 0.00 5.69
73 74 1.079405 GCCTGTTACTGCTGCGGTA 60.079 57.895 17.00 17.00 0.00 4.02
74 75 1.084370 GCCTGTTACTGCTGCGGTAG 61.084 60.000 19.64 9.34 0.00 3.18
76 77 1.475280 CCTGTTACTGCTGCGGTAGTA 59.525 52.381 18.37 18.37 39.12 1.82
78 79 2.163815 CTGTTACTGCTGCGGTAGTACT 59.836 50.000 21.48 0.00 39.64 2.73
79 80 3.346315 TGTTACTGCTGCGGTAGTACTA 58.654 45.455 21.48 11.55 39.64 1.82
82 83 2.015587 ACTGCTGCGGTAGTACTAGTC 58.984 52.381 15.29 0.00 36.66 2.59
83 84 1.334243 CTGCTGCGGTAGTACTAGTCC 59.666 57.143 1.87 0.97 0.00 3.85
84 85 1.340308 TGCTGCGGTAGTACTAGTCCA 60.340 52.381 1.87 0.00 0.00 4.02
86 87 2.915349 CTGCGGTAGTACTAGTCCAGA 58.085 52.381 1.87 0.00 0.00 3.86
88 89 2.026915 TGCGGTAGTACTAGTCCAGACA 60.027 50.000 1.87 0.00 0.00 3.41
89 90 3.012518 GCGGTAGTACTAGTCCAGACAA 58.987 50.000 1.87 0.00 0.00 3.18
91 92 4.497674 GCGGTAGTACTAGTCCAGACAATG 60.498 50.000 1.87 0.00 0.00 2.82
93 94 5.125097 CGGTAGTACTAGTCCAGACAATGTT 59.875 44.000 1.87 0.00 0.00 2.71
94 95 6.349944 CGGTAGTACTAGTCCAGACAATGTTT 60.350 42.308 1.87 0.00 0.00 2.83
95 96 7.384477 GGTAGTACTAGTCCAGACAATGTTTT 58.616 38.462 1.87 0.00 0.00 2.43
99 100 5.437060 ACTAGTCCAGACAATGTTTTGTGT 58.563 37.500 0.00 0.00 46.01 3.72
101 102 7.051623 ACTAGTCCAGACAATGTTTTGTGTTA 58.948 34.615 0.00 0.00 46.01 2.41
102 103 6.767524 AGTCCAGACAATGTTTTGTGTTAA 57.232 33.333 0.00 0.00 46.01 2.01
103 104 7.164230 AGTCCAGACAATGTTTTGTGTTAAA 57.836 32.000 0.00 0.00 46.01 1.52
105 106 8.091449 AGTCCAGACAATGTTTTGTGTTAAAAA 58.909 29.630 0.00 0.00 46.01 1.94
106 107 8.166066 GTCCAGACAATGTTTTGTGTTAAAAAC 58.834 33.333 5.76 5.76 46.01 2.43
107 108 8.091449 TCCAGACAATGTTTTGTGTTAAAAACT 58.909 29.630 12.28 0.00 46.01 2.66
108 109 8.716909 CCAGACAATGTTTTGTGTTAAAAACTT 58.283 29.630 12.28 5.05 46.01 2.66
192 193 4.206477 GGTATTTAGTGGTTACCGTGGT 57.794 45.455 0.00 0.00 0.00 4.16
193 194 4.578871 GGTATTTAGTGGTTACCGTGGTT 58.421 43.478 0.00 0.00 0.00 3.67
195 196 6.348498 GGTATTTAGTGGTTACCGTGGTTAT 58.652 40.000 0.00 0.00 0.00 1.89
196 197 6.479990 GGTATTTAGTGGTTACCGTGGTTATC 59.520 42.308 0.00 0.00 0.00 1.75
197 198 2.660189 AGTGGTTACCGTGGTTATCG 57.340 50.000 0.00 0.00 0.00 2.92
198 199 2.170166 AGTGGTTACCGTGGTTATCGA 58.830 47.619 0.00 0.00 0.00 3.59
200 201 2.094545 GTGGTTACCGTGGTTATCGAGT 60.095 50.000 0.00 0.00 0.00 4.18
201 202 2.562298 TGGTTACCGTGGTTATCGAGTT 59.438 45.455 0.00 0.00 0.00 3.01
202 203 3.006752 TGGTTACCGTGGTTATCGAGTTT 59.993 43.478 0.00 0.00 0.00 2.66
204 205 4.562789 GGTTACCGTGGTTATCGAGTTTAC 59.437 45.833 0.00 0.00 0.00 2.01
205 206 3.236632 ACCGTGGTTATCGAGTTTACC 57.763 47.619 0.00 0.00 0.00 2.85
207 208 1.585214 CGTGGTTATCGAGTTTACCGC 59.415 52.381 10.02 10.02 37.71 5.68
208 209 1.929169 GTGGTTATCGAGTTTACCGCC 59.071 52.381 9.26 0.00 35.62 6.13
210 211 1.575244 GTTATCGAGTTTACCGCCCC 58.425 55.000 0.00 0.00 0.00 5.80
211 212 0.465287 TTATCGAGTTTACCGCCCCC 59.535 55.000 0.00 0.00 0.00 5.40
229 230 4.953940 CCCCCTTGAGAAAAATGTTTCA 57.046 40.909 10.98 0.00 44.82 2.69
230 231 5.488262 CCCCCTTGAGAAAAATGTTTCAT 57.512 39.130 10.98 0.00 44.82 2.57
231 232 5.868454 CCCCCTTGAGAAAAATGTTTCATT 58.132 37.500 10.98 0.00 44.82 2.57
232 233 5.934043 CCCCCTTGAGAAAAATGTTTCATTC 59.066 40.000 10.98 1.38 44.82 2.67
233 234 5.634859 CCCCTTGAGAAAAATGTTTCATTCG 59.365 40.000 10.98 0.00 44.82 3.34
234 235 5.634859 CCCTTGAGAAAAATGTTTCATTCGG 59.365 40.000 10.98 5.67 44.82 4.30
235 236 6.446318 CCTTGAGAAAAATGTTTCATTCGGA 58.554 36.000 10.98 0.00 44.82 4.55
237 238 7.599998 CCTTGAGAAAAATGTTTCATTCGGAAT 59.400 33.333 10.98 0.00 44.82 3.01
238 239 8.885494 TTGAGAAAAATGTTTCATTCGGAATT 57.115 26.923 10.98 0.00 44.82 2.17
239 240 8.519492 TGAGAAAAATGTTTCATTCGGAATTC 57.481 30.769 10.98 0.00 44.82 2.17
240 241 8.140628 TGAGAAAAATGTTTCATTCGGAATTCA 58.859 29.630 10.98 0.00 44.82 2.57
241 242 8.885494 AGAAAAATGTTTCATTCGGAATTCAA 57.115 26.923 10.98 0.00 44.82 2.69
243 244 9.928236 GAAAAATGTTTCATTCGGAATTCAAAA 57.072 25.926 7.93 0.95 42.40 2.44
244 245 9.715123 AAAAATGTTTCATTCGGAATTCAAAAC 57.285 25.926 17.70 17.70 34.91 2.43
247 248 6.578023 TGTTTCATTCGGAATTCAAAACCTT 58.422 32.000 19.77 0.00 34.91 3.50
248 249 6.478344 TGTTTCATTCGGAATTCAAAACCTTG 59.522 34.615 19.77 3.69 34.91 3.61
249 250 6.398234 TTCATTCGGAATTCAAAACCTTGA 57.602 33.333 7.93 0.00 39.87 3.02
262 263 5.705441 TCAAAACCTTGAACTGGCTACATAG 59.295 40.000 0.00 0.00 38.65 2.23
281 282 2.596346 AGAACATCCACACATTGCCAA 58.404 42.857 0.00 0.00 0.00 4.52
295 296 2.799126 TGCCAATCTTCCACGGTATT 57.201 45.000 0.00 0.00 0.00 1.89
296 297 3.916359 TGCCAATCTTCCACGGTATTA 57.084 42.857 0.00 0.00 0.00 0.98
297 298 4.223556 TGCCAATCTTCCACGGTATTAA 57.776 40.909 0.00 0.00 0.00 1.40
298 299 4.787551 TGCCAATCTTCCACGGTATTAAT 58.212 39.130 0.00 0.00 0.00 1.40
299 300 5.197451 TGCCAATCTTCCACGGTATTAATT 58.803 37.500 0.00 0.00 0.00 1.40
300 301 6.358178 TGCCAATCTTCCACGGTATTAATTA 58.642 36.000 0.00 0.00 0.00 1.40
301 302 6.829298 TGCCAATCTTCCACGGTATTAATTAA 59.171 34.615 0.00 0.00 0.00 1.40
302 303 7.504238 TGCCAATCTTCCACGGTATTAATTAAT 59.496 33.333 14.86 14.86 0.00 1.40
303 304 8.357402 GCCAATCTTCCACGGTATTAATTAATT 58.643 33.333 15.64 5.89 0.00 1.40
311 358 9.635404 TCCACGGTATTAATTAATTTGGAGATT 57.365 29.630 15.64 0.00 0.00 2.40
319 366 5.999205 ATTAATTTGGAGATTGTGTGGCA 57.001 34.783 0.00 0.00 0.00 4.92
328 375 1.805428 ATTGTGTGGCAGTTTCCGGC 61.805 55.000 0.00 0.00 0.00 6.13
336 383 1.898574 CAGTTTCCGGCAAGGCAGT 60.899 57.895 0.00 0.00 40.77 4.40
350 397 4.513442 CAAGGCAGTGCATAGTTTACCTA 58.487 43.478 18.61 0.00 0.00 3.08
380 427 2.661718 TGGAAGGGGTGAAGAAACAAC 58.338 47.619 0.00 0.00 0.00 3.32
397 444 1.810755 CAACTCTGCATGCAGTGTGAT 59.189 47.619 40.66 29.31 46.07 3.06
445 1725 0.603707 ACGACCACCAGCTCATTGTG 60.604 55.000 0.00 0.00 0.00 3.33
476 2422 3.888424 TGCAAGCCAGATATGCAGT 57.112 47.368 0.00 0.00 44.52 4.40
481 2427 3.249559 GCAAGCCAGATATGCAGTACTTC 59.750 47.826 0.00 0.00 39.81 3.01
508 2454 3.243704 GCTCAGCGAATCCTTGATACTCT 60.244 47.826 0.00 0.00 0.00 3.24
509 2455 4.545610 CTCAGCGAATCCTTGATACTCTC 58.454 47.826 0.00 0.00 0.00 3.20
522 2468 6.432783 CCTTGATACTCTCCTATCCTACTGTG 59.567 46.154 0.00 0.00 0.00 3.66
523 2469 5.317808 TGATACTCTCCTATCCTACTGTGC 58.682 45.833 0.00 0.00 0.00 4.57
532 2497 0.809385 TCCTACTGTGCGAGTGTAGC 59.191 55.000 0.00 0.00 35.96 3.58
589 4238 1.412250 TATAAAACCACGCGCCGACG 61.412 55.000 5.73 0.00 44.07 5.12
639 4334 4.950475 TGTCATGACTATCTCTCCGTTTCT 59.050 41.667 25.55 0.00 0.00 2.52
682 4377 7.459234 TCCATGCTCAAGAATCAAGATGATAT 58.541 34.615 0.00 0.00 35.76 1.63
840 4588 4.514441 CGTCCGAAAGCCTCTATAAGTAGA 59.486 45.833 0.00 0.00 35.67 2.59
856 4604 4.558226 AGTAGATCATGTTTGCCTGTGA 57.442 40.909 0.00 0.00 0.00 3.58
875 8447 2.094906 TGAATCTCTGCATTGCAAGCAC 60.095 45.455 13.18 8.79 38.41 4.40
905 8478 8.312564 AGTAACAGTTCTATTCCTAGTTTGTCC 58.687 37.037 0.00 0.00 0.00 4.02
910 8483 2.693267 ATTCCTAGTTTGTCCCTCGC 57.307 50.000 0.00 0.00 0.00 5.03
917 8490 1.154197 GTTTGTCCCTCGCTTGGTAC 58.846 55.000 0.00 0.00 0.00 3.34
919 8492 0.034337 TTGTCCCTCGCTTGGTACAC 59.966 55.000 0.00 0.00 39.29 2.90
922 8495 0.830444 TCCCTCGCTTGGTACACAGT 60.830 55.000 0.00 0.00 39.29 3.55
927 8500 1.542915 TCGCTTGGTACACAGTACTCC 59.457 52.381 7.19 0.00 39.29 3.85
928 8501 1.544691 CGCTTGGTACACAGTACTCCT 59.455 52.381 7.19 0.00 39.29 3.69
929 8502 2.751259 CGCTTGGTACACAGTACTCCTA 59.249 50.000 7.19 0.00 39.29 2.94
930 8503 3.427233 CGCTTGGTACACAGTACTCCTAC 60.427 52.174 7.19 0.00 39.29 3.18
931 8504 3.508793 GCTTGGTACACAGTACTCCTACA 59.491 47.826 7.19 0.00 39.29 2.74
932 8505 4.617762 GCTTGGTACACAGTACTCCTACAC 60.618 50.000 7.19 0.00 39.29 2.90
938 8522 4.481072 ACACAGTACTCCTACACCTCTTT 58.519 43.478 0.00 0.00 0.00 2.52
948 8532 6.099845 ACTCCTACACCTCTTTGAAAGAAAGA 59.900 38.462 9.15 0.00 37.02 2.52
951 8535 6.936900 CCTACACCTCTTTGAAAGAAAGATCA 59.063 38.462 9.15 0.00 37.02 2.92
952 8536 6.625873 ACACCTCTTTGAAAGAAAGATCAC 57.374 37.500 9.15 0.00 37.02 3.06
953 8537 5.532779 ACACCTCTTTGAAAGAAAGATCACC 59.467 40.000 9.15 0.00 37.02 4.02
954 8538 5.767168 CACCTCTTTGAAAGAAAGATCACCT 59.233 40.000 9.15 0.00 37.02 4.00
981 8573 0.659957 CCTACGTACGTAGTGCCTCC 59.340 60.000 38.99 0.00 45.73 4.30
984 8576 2.048023 CGTACGTAGTGCCTCCCCA 61.048 63.158 7.22 0.00 45.73 4.96
990 8584 0.958876 GTAGTGCCTCCCCAAAACCG 60.959 60.000 0.00 0.00 0.00 4.44
996 8590 1.149627 CTCCCCAAAACCGTGACCA 59.850 57.895 0.00 0.00 0.00 4.02
1059 8653 1.999071 TTGCGTGTTGTGCCCTTGTC 61.999 55.000 0.00 0.00 0.00 3.18
1074 8668 0.970937 TTGTCCAGAGCTCCTACGGG 60.971 60.000 10.93 4.89 0.00 5.28
1177 9072 1.538849 CGACCGATCATCATGGAGCAA 60.539 52.381 0.00 0.00 0.00 3.91
1185 9095 1.674441 CATCATGGAGCAAACGCTGAT 59.326 47.619 0.00 0.00 40.78 2.90
1187 9097 1.089112 CATGGAGCAAACGCTGATGA 58.911 50.000 0.00 0.00 40.78 2.92
1196 9106 0.677731 AACGCTGATGATGGTGGTGG 60.678 55.000 0.00 0.00 0.00 4.61
1198 9108 1.371337 CGCTGATGATGGTGGTGGTG 61.371 60.000 0.00 0.00 0.00 4.17
1199 9109 1.660560 GCTGATGATGGTGGTGGTGC 61.661 60.000 0.00 0.00 0.00 5.01
1200 9110 0.034767 CTGATGATGGTGGTGGTGCT 60.035 55.000 0.00 0.00 0.00 4.40
1201 9111 0.035152 TGATGATGGTGGTGGTGCTC 60.035 55.000 0.00 0.00 0.00 4.26
1202 9112 0.749454 GATGATGGTGGTGGTGCTCC 60.749 60.000 0.00 0.00 0.00 4.70
1203 9113 1.210204 ATGATGGTGGTGGTGCTCCT 61.210 55.000 6.34 0.00 34.23 3.69
1204 9114 1.377725 GATGGTGGTGGTGCTCCTG 60.378 63.158 6.34 0.00 34.23 3.86
1205 9115 3.574074 ATGGTGGTGGTGCTCCTGC 62.574 63.158 6.34 0.00 40.20 4.85
1215 9125 2.256461 GCTCCTGCAACTTTGGCG 59.744 61.111 0.00 0.00 39.41 5.69
1216 9126 2.260869 GCTCCTGCAACTTTGGCGA 61.261 57.895 0.00 0.00 39.41 5.54
1217 9127 1.589716 GCTCCTGCAACTTTGGCGAT 61.590 55.000 0.00 0.00 39.41 4.58
1218 9128 0.169672 CTCCTGCAACTTTGGCGATG 59.830 55.000 0.00 0.00 0.00 3.84
1219 9129 1.213537 CCTGCAACTTTGGCGATGG 59.786 57.895 0.00 0.00 0.00 3.51
1220 9130 1.213537 CTGCAACTTTGGCGATGGG 59.786 57.895 0.00 0.00 0.00 4.00
1221 9131 2.125952 GCAACTTTGGCGATGGGC 60.126 61.111 0.00 0.00 42.51 5.36
1222 9132 2.179018 CAACTTTGGCGATGGGCG 59.821 61.111 0.00 0.00 44.92 6.13
1223 9133 2.033448 AACTTTGGCGATGGGCGA 59.967 55.556 0.00 0.00 44.92 5.54
1224 9134 2.040544 AACTTTGGCGATGGGCGAG 61.041 57.895 0.00 0.13 44.92 5.03
1225 9135 3.204827 CTTTGGCGATGGGCGAGG 61.205 66.667 0.00 0.00 44.92 4.63
1236 9146 4.752879 GGCGAGGCTGGCGTTGTA 62.753 66.667 15.46 0.00 0.00 2.41
1251 9161 1.400846 GTTGTATCGTCGGAGCAGAGA 59.599 52.381 0.00 0.00 0.00 3.10
1380 9290 2.124529 TGCCACTCCAACAACGCA 60.125 55.556 0.00 0.00 0.00 5.24
1473 9384 5.066893 CCCAGTTGATTCATTCATCGTTGAT 59.933 40.000 0.00 0.00 33.34 2.57
1488 9406 4.565022 TCGTTGATGCTTTCATGACACTA 58.435 39.130 0.00 0.00 33.34 2.74
1512 9430 7.553881 AGAACTTTCGATCTTGTTCTTTCAA 57.446 32.000 13.39 0.00 44.32 2.69
1514 9432 8.125448 AGAACTTTCGATCTTGTTCTTTCAAAG 58.875 33.333 13.39 0.00 44.32 2.77
1520 9438 5.341462 CGATCTTGTTCTTTCAAAGCATGTG 59.659 40.000 0.00 0.00 0.00 3.21
1521 9439 5.581126 TCTTGTTCTTTCAAAGCATGTGT 57.419 34.783 0.00 0.00 0.00 3.72
1522 9440 5.581605 TCTTGTTCTTTCAAAGCATGTGTC 58.418 37.500 0.00 0.00 0.00 3.67
1523 9441 5.357878 TCTTGTTCTTTCAAAGCATGTGTCT 59.642 36.000 0.00 0.00 0.00 3.41
1524 9442 4.923893 TGTTCTTTCAAAGCATGTGTCTG 58.076 39.130 0.00 0.00 0.00 3.51
1601 9525 8.814038 AAGATTGCCTCATCTGTTAATTAAGT 57.186 30.769 0.00 0.00 0.00 2.24
1602 9526 8.443953 AGATTGCCTCATCTGTTAATTAAGTC 57.556 34.615 0.00 0.00 0.00 3.01
1614 9538 9.706691 TCTGTTAATTAAGTCGAAGAGAATTGT 57.293 29.630 0.00 0.00 37.74 2.71
1663 9587 0.879090 CCGGAACAACAAGGGCTAAC 59.121 55.000 0.00 0.00 0.00 2.34
1721 9649 1.270625 ACGACCAACACCGATGACAAT 60.271 47.619 0.00 0.00 0.00 2.71
1749 9677 1.157870 CCACACGACACAAGGTCCAC 61.158 60.000 0.00 0.00 43.95 4.02
1956 9884 3.722295 CGAACGCCGCACCACATT 61.722 61.111 0.00 0.00 0.00 2.71
2012 9940 2.502510 GCATCAACGCCGCACAAG 60.503 61.111 0.00 0.00 0.00 3.16
2048 9976 1.611410 CCATGCTGCACAGGACAACTA 60.611 52.381 15.70 0.00 29.21 2.24
2066 9997 2.028112 ACTACATGCAGACCACGAATGT 60.028 45.455 0.00 0.00 35.70 2.71
2114 10045 1.902556 GTAAAGTCAGGCCGCCCTA 59.097 57.895 5.55 0.00 40.33 3.53
2119 10050 2.134287 GTCAGGCCGCCCTATCTGA 61.134 63.158 5.55 0.00 40.33 3.27
2121 10052 1.834378 CAGGCCGCCCTATCTGAGA 60.834 63.158 5.55 0.00 40.33 3.27
2213 10145 1.340399 CCCCACCTCATAGAGCTGCA 61.340 60.000 1.02 0.00 0.00 4.41
2231 10163 0.871722 CAACTCGCATTGTTCCCGAA 59.128 50.000 0.00 0.00 0.00 4.30
2236 10168 0.446222 CGCATTGTTCCCGAAATCGT 59.554 50.000 1.79 0.00 37.74 3.73
2265 10197 0.820871 GCACAAACAGAAACCACCCA 59.179 50.000 0.00 0.00 0.00 4.51
2269 10201 2.025321 ACAAACAGAAACCACCCAGAGT 60.025 45.455 0.00 0.00 0.00 3.24
2271 10203 0.765510 ACAGAAACCACCCAGAGTCC 59.234 55.000 0.00 0.00 0.00 3.85
2309 10241 2.036733 TGTTCCCGACGACAAAGAGATT 59.963 45.455 0.00 0.00 0.00 2.40
2310 10242 2.649331 TCCCGACGACAAAGAGATTC 57.351 50.000 0.00 0.00 0.00 2.52
2311 10243 1.890489 TCCCGACGACAAAGAGATTCA 59.110 47.619 0.00 0.00 0.00 2.57
2312 10244 2.496070 TCCCGACGACAAAGAGATTCAT 59.504 45.455 0.00 0.00 0.00 2.57
2313 10245 2.604914 CCCGACGACAAAGAGATTCATG 59.395 50.000 0.00 0.00 0.00 3.07
2314 10246 3.511699 CCGACGACAAAGAGATTCATGA 58.488 45.455 0.00 0.00 0.00 3.07
2315 10247 3.549471 CCGACGACAAAGAGATTCATGAG 59.451 47.826 0.00 0.00 0.00 2.90
2316 10248 4.415735 CGACGACAAAGAGATTCATGAGA 58.584 43.478 0.00 0.00 0.00 3.27
2335 10267 4.170256 GAGACCTCTTTGATTCACTCGTC 58.830 47.826 0.00 0.00 0.00 4.20
2364 10296 6.831769 ACGCTTTCATGTAAATCAACAGTAG 58.168 36.000 0.00 0.00 31.70 2.57
2383 10315 1.817447 AGCAGCTCTTTCCAATCTTGC 59.183 47.619 0.00 0.00 0.00 4.01
2389 10327 3.181512 GCTCTTTCCAATCTTGCTCTTCG 60.182 47.826 0.00 0.00 0.00 3.79
2411 10349 5.982516 TCGAAAAATGTGAACCCTTTCATTG 59.017 36.000 0.00 0.00 43.72 2.82
2412 10350 5.752955 CGAAAAATGTGAACCCTTTCATTGT 59.247 36.000 0.00 0.00 43.72 2.71
2413 10351 6.257630 CGAAAAATGTGAACCCTTTCATTGTT 59.742 34.615 0.00 0.00 43.72 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.122150 CTGGACGATTTGCAGACGA 57.878 52.632 14.13 0.00 46.53 4.20
15 16 1.461127 GACACACTCTGGACGATTTGC 59.539 52.381 0.00 0.00 0.00 3.68
16 17 1.721389 CGACACACTCTGGACGATTTG 59.279 52.381 0.00 0.00 0.00 2.32
18 19 0.959553 ACGACACACTCTGGACGATT 59.040 50.000 0.00 0.00 0.00 3.34
19 20 0.959553 AACGACACACTCTGGACGAT 59.040 50.000 0.00 0.00 0.00 3.73
20 21 0.742505 AAACGACACACTCTGGACGA 59.257 50.000 0.00 0.00 0.00 4.20
21 22 0.852777 CAAACGACACACTCTGGACG 59.147 55.000 0.00 0.00 0.00 4.79
22 23 1.593006 CACAAACGACACACTCTGGAC 59.407 52.381 0.00 0.00 0.00 4.02
23 24 1.206132 ACACAAACGACACACTCTGGA 59.794 47.619 0.00 0.00 0.00 3.86
26 27 2.159156 TGCTACACAAACGACACACTCT 60.159 45.455 0.00 0.00 0.00 3.24
29 30 1.661617 TGTGCTACACAAACGACACAC 59.338 47.619 0.00 0.00 41.69 3.82
30 31 1.930503 CTGTGCTACACAAACGACACA 59.069 47.619 1.64 0.00 44.08 3.72
31 32 1.332904 GCTGTGCTACACAAACGACAC 60.333 52.381 1.64 0.00 44.08 3.67
32 33 0.934496 GCTGTGCTACACAAACGACA 59.066 50.000 1.64 0.00 44.08 4.35
33 34 1.192534 GAGCTGTGCTACACAAACGAC 59.807 52.381 0.00 0.00 44.08 4.34
34 35 1.497991 GAGCTGTGCTACACAAACGA 58.502 50.000 0.00 0.00 44.08 3.85
35 36 0.161658 CGAGCTGTGCTACACAAACG 59.838 55.000 0.00 4.60 44.08 3.60
37 38 1.227999 GCCGAGCTGTGCTACACAAA 61.228 55.000 0.00 0.00 44.08 2.83
38 39 1.667830 GCCGAGCTGTGCTACACAA 60.668 57.895 0.00 0.00 44.08 3.33
39 40 2.048222 GCCGAGCTGTGCTACACA 60.048 61.111 0.00 0.00 42.45 3.72
40 41 2.815647 GGCCGAGCTGTGCTACAC 60.816 66.667 0.00 0.00 39.88 2.90
41 42 2.997315 AGGCCGAGCTGTGCTACA 60.997 61.111 0.00 0.00 39.88 2.74
45 46 2.047274 TAACAGGCCGAGCTGTGC 60.047 61.111 0.00 0.00 33.66 4.57
46 47 1.016130 CAGTAACAGGCCGAGCTGTG 61.016 60.000 0.00 0.00 33.66 3.66
47 48 1.293498 CAGTAACAGGCCGAGCTGT 59.707 57.895 0.00 0.00 35.00 4.40
48 49 2.103042 GCAGTAACAGGCCGAGCTG 61.103 63.158 0.00 4.30 0.00 4.24
49 50 2.266055 GCAGTAACAGGCCGAGCT 59.734 61.111 0.00 0.00 0.00 4.09
52 53 2.047274 GCAGCAGTAACAGGCCGA 60.047 61.111 0.00 0.00 0.00 5.54
54 55 2.515996 TACCGCAGCAGTAACAGGCC 62.516 60.000 0.00 0.00 0.00 5.19
55 56 1.079405 TACCGCAGCAGTAACAGGC 60.079 57.895 0.00 0.00 0.00 4.85
57 58 2.163815 AGTACTACCGCAGCAGTAACAG 59.836 50.000 0.00 0.00 0.00 3.16
58 59 2.165167 AGTACTACCGCAGCAGTAACA 58.835 47.619 0.00 0.00 0.00 2.41
59 60 2.935481 AGTACTACCGCAGCAGTAAC 57.065 50.000 0.00 0.00 0.00 2.50
60 61 3.614092 ACTAGTACTACCGCAGCAGTAA 58.386 45.455 0.00 0.00 0.00 2.24
62 63 2.015587 GACTAGTACTACCGCAGCAGT 58.984 52.381 0.00 0.00 0.00 4.40
63 64 1.334243 GGACTAGTACTACCGCAGCAG 59.666 57.143 0.00 0.00 0.00 4.24
64 65 1.340308 TGGACTAGTACTACCGCAGCA 60.340 52.381 6.66 0.00 0.00 4.41
65 66 1.334243 CTGGACTAGTACTACCGCAGC 59.666 57.143 6.66 0.00 0.00 5.25
66 67 2.613133 GTCTGGACTAGTACTACCGCAG 59.387 54.545 6.66 0.00 0.00 5.18
67 68 2.026915 TGTCTGGACTAGTACTACCGCA 60.027 50.000 6.66 0.00 0.00 5.69
68 69 2.636830 TGTCTGGACTAGTACTACCGC 58.363 52.381 6.66 0.00 0.00 5.68
69 70 4.639310 ACATTGTCTGGACTAGTACTACCG 59.361 45.833 6.66 0.00 0.00 4.02
70 71 6.527057 AACATTGTCTGGACTAGTACTACC 57.473 41.667 6.66 0.33 0.00 3.18
71 72 7.871463 ACAAAACATTGTCTGGACTAGTACTAC 59.129 37.037 6.66 5.49 0.00 2.73
73 74 6.706270 CACAAAACATTGTCTGGACTAGTACT 59.294 38.462 6.66 0.00 31.86 2.73
74 75 6.482308 ACACAAAACATTGTCTGGACTAGTAC 59.518 38.462 0.00 0.00 31.86 2.73
76 77 5.437060 ACACAAAACATTGTCTGGACTAGT 58.563 37.500 0.00 0.00 31.86 2.57
78 79 7.867305 TTAACACAAAACATTGTCTGGACTA 57.133 32.000 2.38 0.00 31.86 2.59
79 80 6.767524 TTAACACAAAACATTGTCTGGACT 57.232 33.333 2.38 0.00 31.86 3.85
82 83 8.250538 AGTTTTTAACACAAAACATTGTCTGG 57.749 30.769 10.73 0.00 45.43 3.86
95 96 9.866936 GACACGAATACATAAGTTTTTAACACA 57.133 29.630 0.00 0.00 0.00 3.72
171 172 4.206477 ACCACGGTAACCACTAAATACC 57.794 45.455 0.00 0.00 36.54 2.73
173 174 6.096141 TCGATAACCACGGTAACCACTAAATA 59.904 38.462 0.00 0.00 0.00 1.40
174 175 5.105392 TCGATAACCACGGTAACCACTAAAT 60.105 40.000 0.00 0.00 0.00 1.40
175 176 4.219507 TCGATAACCACGGTAACCACTAAA 59.780 41.667 0.00 0.00 0.00 1.85
176 177 3.761218 TCGATAACCACGGTAACCACTAA 59.239 43.478 0.00 0.00 0.00 2.24
177 178 3.351740 TCGATAACCACGGTAACCACTA 58.648 45.455 0.00 0.00 0.00 2.74
178 179 2.165030 CTCGATAACCACGGTAACCACT 59.835 50.000 0.00 0.00 0.00 4.00
179 180 2.094545 ACTCGATAACCACGGTAACCAC 60.095 50.000 0.00 0.00 0.00 4.16
180 181 2.170166 ACTCGATAACCACGGTAACCA 58.830 47.619 0.00 0.00 0.00 3.67
181 182 2.947448 ACTCGATAACCACGGTAACC 57.053 50.000 0.00 0.00 0.00 2.85
183 184 4.674101 CGGTAAACTCGATAACCACGGTAA 60.674 45.833 0.00 0.00 32.04 2.85
184 185 3.181501 CGGTAAACTCGATAACCACGGTA 60.182 47.826 0.00 0.00 32.04 4.02
185 186 2.415893 CGGTAAACTCGATAACCACGGT 60.416 50.000 0.00 0.00 32.04 4.83
188 189 1.929169 GGCGGTAAACTCGATAACCAC 59.071 52.381 0.00 0.00 32.04 4.16
189 190 1.134729 GGGCGGTAAACTCGATAACCA 60.135 52.381 0.00 0.00 32.04 3.67
192 193 0.465287 GGGGGCGGTAAACTCGATAA 59.535 55.000 0.00 0.00 0.00 1.75
193 194 2.126951 GGGGGCGGTAAACTCGATA 58.873 57.895 0.00 0.00 0.00 2.92
208 209 4.953940 TGAAACATTTTTCTCAAGGGGG 57.046 40.909 5.95 0.00 41.64 5.40
210 211 5.634859 CCGAATGAAACATTTTTCTCAAGGG 59.365 40.000 5.95 0.00 41.64 3.95
211 212 6.446318 TCCGAATGAAACATTTTTCTCAAGG 58.554 36.000 5.95 5.01 41.64 3.61
214 215 8.140628 TGAATTCCGAATGAAACATTTTTCTCA 58.859 29.630 2.27 0.00 41.64 3.27
216 217 8.885494 TTGAATTCCGAATGAAACATTTTTCT 57.115 26.923 2.27 0.00 41.64 2.52
217 218 9.928236 TTTTGAATTCCGAATGAAACATTTTTC 57.072 25.926 2.27 0.00 41.49 2.29
219 220 8.341903 GGTTTTGAATTCCGAATGAAACATTTT 58.658 29.630 19.27 0.00 36.33 1.82
220 221 7.714813 AGGTTTTGAATTCCGAATGAAACATTT 59.285 29.630 19.27 9.34 36.33 2.32
222 223 6.758254 AGGTTTTGAATTCCGAATGAAACAT 58.242 32.000 19.27 14.17 36.33 2.71
223 224 6.155475 AGGTTTTGAATTCCGAATGAAACA 57.845 33.333 19.27 7.73 36.33 2.83
225 226 6.810911 TCAAGGTTTTGAATTCCGAATGAAA 58.189 32.000 2.27 0.00 40.26 2.69
226 227 6.398234 TCAAGGTTTTGAATTCCGAATGAA 57.602 33.333 2.27 0.00 40.26 2.57
238 239 3.892284 TGTAGCCAGTTCAAGGTTTTGA 58.108 40.909 0.00 0.00 41.44 2.69
239 240 4.853924 ATGTAGCCAGTTCAAGGTTTTG 57.146 40.909 0.00 0.00 35.57 2.44
240 241 5.876357 TCTATGTAGCCAGTTCAAGGTTTT 58.124 37.500 0.00 0.00 0.00 2.43
241 242 5.499004 TCTATGTAGCCAGTTCAAGGTTT 57.501 39.130 0.00 0.00 0.00 3.27
243 244 4.286032 TGTTCTATGTAGCCAGTTCAAGGT 59.714 41.667 0.00 0.00 0.00 3.50
244 245 4.832248 TGTTCTATGTAGCCAGTTCAAGG 58.168 43.478 0.00 0.00 0.00 3.61
247 248 4.469586 TGGATGTTCTATGTAGCCAGTTCA 59.530 41.667 0.00 0.00 0.00 3.18
248 249 4.811557 GTGGATGTTCTATGTAGCCAGTTC 59.188 45.833 0.00 0.00 0.00 3.01
249 250 4.225042 TGTGGATGTTCTATGTAGCCAGTT 59.775 41.667 0.00 0.00 0.00 3.16
252 253 3.517500 TGTGTGGATGTTCTATGTAGCCA 59.482 43.478 0.00 0.00 0.00 4.75
254 255 5.504665 GCAATGTGTGGATGTTCTATGTAGC 60.505 44.000 0.00 0.00 0.00 3.58
262 263 3.194116 AGATTGGCAATGTGTGGATGTTC 59.806 43.478 19.07 0.00 0.00 3.18
281 282 9.635404 TCCAAATTAATTAATACCGTGGAAGAT 57.365 29.630 20.06 0.01 0.00 2.40
295 296 7.178274 ACTGCCACACAATCTCCAAATTAATTA 59.822 33.333 0.01 0.00 0.00 1.40
296 297 6.014327 ACTGCCACACAATCTCCAAATTAATT 60.014 34.615 0.00 0.00 0.00 1.40
297 298 5.481473 ACTGCCACACAATCTCCAAATTAAT 59.519 36.000 0.00 0.00 0.00 1.40
298 299 4.832266 ACTGCCACACAATCTCCAAATTAA 59.168 37.500 0.00 0.00 0.00 1.40
299 300 4.406456 ACTGCCACACAATCTCCAAATTA 58.594 39.130 0.00 0.00 0.00 1.40
300 301 3.233507 ACTGCCACACAATCTCCAAATT 58.766 40.909 0.00 0.00 0.00 1.82
301 302 2.880443 ACTGCCACACAATCTCCAAAT 58.120 42.857 0.00 0.00 0.00 2.32
302 303 2.363306 ACTGCCACACAATCTCCAAA 57.637 45.000 0.00 0.00 0.00 3.28
303 304 2.363306 AACTGCCACACAATCTCCAA 57.637 45.000 0.00 0.00 0.00 3.53
311 358 2.904866 GCCGGAAACTGCCACACA 60.905 61.111 5.05 0.00 34.03 3.72
319 366 1.898574 CACTGCCTTGCCGGAAACT 60.899 57.895 5.05 0.00 33.16 2.66
328 375 3.347216 AGGTAAACTATGCACTGCCTTG 58.653 45.455 0.00 0.00 0.00 3.61
350 397 2.311542 TCACCCCTTCCATGCATAGTTT 59.688 45.455 0.00 0.00 0.00 2.66
380 427 1.015109 GGATCACACTGCATGCAGAG 58.985 55.000 45.50 39.79 46.30 3.35
397 444 1.339055 GCATAGGAGCACACAAGTGGA 60.339 52.381 5.08 0.00 45.98 4.02
445 1725 4.580995 TCTGGCTTGCAGAGTAGAGTATAC 59.419 45.833 0.00 0.00 0.00 1.47
476 2422 3.066900 GGATTCGCTGAGCTGTAGAAGTA 59.933 47.826 1.78 0.00 0.00 2.24
481 2427 2.159184 TCAAGGATTCGCTGAGCTGTAG 60.159 50.000 1.78 0.00 0.00 2.74
508 2454 2.298610 CACTCGCACAGTAGGATAGGA 58.701 52.381 0.00 0.00 32.21 2.94
509 2455 2.025155 ACACTCGCACAGTAGGATAGG 58.975 52.381 0.00 0.00 32.21 2.57
522 2468 5.181622 AGGAATATACTACTGCTACACTCGC 59.818 44.000 0.00 0.00 0.00 5.03
523 2469 6.401260 CGAGGAATATACTACTGCTACACTCG 60.401 46.154 0.00 0.00 36.19 4.18
532 2497 6.153067 CCTTTCTGCGAGGAATATACTACTG 58.847 44.000 0.00 0.00 36.33 2.74
614 4263 5.661056 AACGGAGAGATAGTCATGACAAA 57.339 39.130 27.02 15.21 0.00 2.83
615 4264 5.419155 AGAAACGGAGAGATAGTCATGACAA 59.581 40.000 27.02 0.00 0.00 3.18
616 4265 4.950475 AGAAACGGAGAGATAGTCATGACA 59.050 41.667 27.02 13.67 0.00 3.58
617 4266 5.508200 AGAAACGGAGAGATAGTCATGAC 57.492 43.478 18.47 18.47 0.00 3.06
618 4267 6.358178 AGTAGAAACGGAGAGATAGTCATGA 58.642 40.000 0.00 0.00 0.00 3.07
621 4270 6.178324 TGAAGTAGAAACGGAGAGATAGTCA 58.822 40.000 0.00 0.00 0.00 3.41
626 4321 6.347859 AGTTTGAAGTAGAAACGGAGAGAT 57.652 37.500 0.00 0.00 38.18 2.75
639 4334 3.550820 TGGAGCAGCAAAGTTTGAAGTA 58.449 40.909 19.82 0.00 0.00 2.24
682 4377 7.555965 AGAATACACTACACATCAGCACATAA 58.444 34.615 0.00 0.00 0.00 1.90
733 4446 0.666274 TTCACCGAGCATGTGACGAC 60.666 55.000 9.15 0.00 42.13 4.34
840 4588 4.398358 CAGAGATTCACAGGCAAACATGAT 59.602 41.667 0.00 0.00 0.00 2.45
875 8447 6.868622 ACTAGGAATAGAACTGTTACTGCAG 58.131 40.000 13.48 13.48 41.92 4.41
905 8478 1.544691 AGTACTGTGTACCAAGCGAGG 59.455 52.381 0.00 0.00 0.00 4.63
910 8483 4.082354 GGTGTAGGAGTACTGTGTACCAAG 60.082 50.000 0.00 0.00 0.00 3.61
917 8490 4.523173 TCAAAGAGGTGTAGGAGTACTGTG 59.477 45.833 0.00 0.00 0.00 3.66
919 8492 5.723672 TTCAAAGAGGTGTAGGAGTACTG 57.276 43.478 0.00 0.00 0.00 2.74
922 8495 6.989155 TTCTTTCAAAGAGGTGTAGGAGTA 57.011 37.500 0.00 0.00 39.03 2.59
927 8500 7.095017 GGTGATCTTTCTTTCAAAGAGGTGTAG 60.095 40.741 0.00 0.00 39.36 2.74
928 8501 6.710744 GGTGATCTTTCTTTCAAAGAGGTGTA 59.289 38.462 0.00 0.00 39.36 2.90
929 8502 5.532779 GGTGATCTTTCTTTCAAAGAGGTGT 59.467 40.000 0.00 0.00 39.36 4.16
930 8503 5.767168 AGGTGATCTTTCTTTCAAAGAGGTG 59.233 40.000 0.00 0.00 39.36 4.00
931 8504 5.946486 AGGTGATCTTTCTTTCAAAGAGGT 58.054 37.500 0.00 0.00 39.36 3.85
932 8505 6.936900 TGTAGGTGATCTTTCTTTCAAAGAGG 59.063 38.462 0.00 0.00 39.36 3.69
938 8522 5.825593 AGGTGTAGGTGATCTTTCTTTCA 57.174 39.130 0.00 0.00 0.00 2.69
948 8532 3.659183 ACGTAGGTAGGTGTAGGTGAT 57.341 47.619 0.00 0.00 0.00 3.06
951 8535 2.236395 ACGTACGTAGGTAGGTGTAGGT 59.764 50.000 21.41 0.00 43.85 3.08
952 8536 2.906354 ACGTACGTAGGTAGGTGTAGG 58.094 52.381 21.41 0.00 43.85 3.18
981 8573 2.674796 TTTTTGGTCACGGTTTTGGG 57.325 45.000 0.00 0.00 0.00 4.12
984 8576 2.093447 TGCCATTTTTGGTCACGGTTTT 60.093 40.909 0.00 0.00 0.00 2.43
990 8584 0.387565 ACCGTGCCATTTTTGGTCAC 59.612 50.000 8.55 8.55 34.75 3.67
996 8590 1.665442 GGAGCACCGTGCCATTTTT 59.335 52.632 19.96 0.00 46.52 1.94
1023 8617 1.788258 CAAGAAGAAGCAGCGTGAGA 58.212 50.000 0.00 0.00 0.00 3.27
1074 8668 3.507009 CGGGGAGACGGTCTCGAC 61.507 72.222 26.86 22.06 44.28 4.20
1177 9072 0.677731 CCACCACCATCATCAGCGTT 60.678 55.000 0.00 0.00 0.00 4.84
1185 9095 1.847506 AGGAGCACCACCACCATCA 60.848 57.895 2.07 0.00 38.94 3.07
1187 9097 2.759114 CAGGAGCACCACCACCAT 59.241 61.111 2.07 0.00 38.94 3.55
1198 9108 1.589716 ATCGCCAAAGTTGCAGGAGC 61.590 55.000 0.00 0.00 42.57 4.70
1199 9109 0.169672 CATCGCCAAAGTTGCAGGAG 59.830 55.000 0.00 0.00 0.00 3.69
1200 9110 1.243342 CCATCGCCAAAGTTGCAGGA 61.243 55.000 0.00 0.00 0.00 3.86
1201 9111 1.213537 CCATCGCCAAAGTTGCAGG 59.786 57.895 0.00 0.00 0.00 4.85
1202 9112 1.213537 CCCATCGCCAAAGTTGCAG 59.786 57.895 0.00 0.00 0.00 4.41
1203 9113 2.929903 GCCCATCGCCAAAGTTGCA 61.930 57.895 0.00 0.00 0.00 4.08
1204 9114 2.125952 GCCCATCGCCAAAGTTGC 60.126 61.111 0.00 0.00 0.00 4.17
1205 9115 2.179018 CGCCCATCGCCAAAGTTG 59.821 61.111 0.00 0.00 0.00 3.16
1206 9116 2.033448 TCGCCCATCGCCAAAGTT 59.967 55.556 0.00 0.00 38.27 2.66
1207 9117 2.436646 CTCGCCCATCGCCAAAGT 60.437 61.111 0.00 0.00 38.27 2.66
1208 9118 3.204827 CCTCGCCCATCGCCAAAG 61.205 66.667 0.00 0.00 38.27 2.77
1219 9129 4.752879 TACAACGCCAGCCTCGCC 62.753 66.667 0.00 0.00 0.00 5.54
1220 9130 2.511600 ATACAACGCCAGCCTCGC 60.512 61.111 0.00 0.00 0.00 5.03
1221 9131 2.230940 CGATACAACGCCAGCCTCG 61.231 63.158 0.00 0.00 0.00 4.63
1222 9132 1.146358 GACGATACAACGCCAGCCTC 61.146 60.000 0.00 0.00 36.70 4.70
1223 9133 1.153628 GACGATACAACGCCAGCCT 60.154 57.895 0.00 0.00 36.70 4.58
1224 9134 2.514013 CGACGATACAACGCCAGCC 61.514 63.158 0.00 0.00 36.70 4.85
1225 9135 2.514013 CCGACGATACAACGCCAGC 61.514 63.158 0.00 0.00 36.70 4.85
1226 9136 0.866061 CTCCGACGATACAACGCCAG 60.866 60.000 0.00 0.00 36.70 4.85
1227 9137 1.138036 CTCCGACGATACAACGCCA 59.862 57.895 0.00 0.00 36.70 5.69
1228 9138 2.228914 GCTCCGACGATACAACGCC 61.229 63.158 0.00 0.00 36.70 5.68
1229 9139 1.472276 CTGCTCCGACGATACAACGC 61.472 60.000 0.00 0.00 36.70 4.84
1230 9140 0.098200 TCTGCTCCGACGATACAACG 59.902 55.000 0.00 0.00 39.31 4.10
1231 9141 1.400846 TCTCTGCTCCGACGATACAAC 59.599 52.381 0.00 0.00 0.00 3.32
1232 9142 1.746470 TCTCTGCTCCGACGATACAA 58.254 50.000 0.00 0.00 0.00 2.41
1233 9143 1.746470 TTCTCTGCTCCGACGATACA 58.254 50.000 0.00 0.00 0.00 2.29
1234 9144 2.541999 CCTTTCTCTGCTCCGACGATAC 60.542 54.545 0.00 0.00 0.00 2.24
1235 9145 1.676529 CCTTTCTCTGCTCCGACGATA 59.323 52.381 0.00 0.00 0.00 2.92
1236 9146 0.457851 CCTTTCTCTGCTCCGACGAT 59.542 55.000 0.00 0.00 0.00 3.73
1251 9161 4.678743 GGCGCCCCTGAACCCTTT 62.679 66.667 18.11 0.00 0.00 3.11
1281 9191 3.406200 AGCATCCTTCCCAGCGCT 61.406 61.111 2.64 2.64 0.00 5.92
1356 9266 4.308458 TTGGAGTGGCACGACGGG 62.308 66.667 12.71 0.00 0.00 5.28
1473 9384 5.177511 CGAAAGTTCTAGTGTCATGAAAGCA 59.822 40.000 0.00 0.00 0.00 3.91
1512 9430 1.209019 CTAGCTCCCAGACACATGCTT 59.791 52.381 0.00 0.00 32.72 3.91
1514 9432 0.813210 GCTAGCTCCCAGACACATGC 60.813 60.000 7.70 0.00 0.00 4.06
1520 9438 1.324383 GGACTAGCTAGCTCCCAGAC 58.676 60.000 23.26 13.36 0.00 3.51
1521 9439 0.179015 CGGACTAGCTAGCTCCCAGA 60.179 60.000 23.26 1.52 0.00 3.86
1522 9440 0.179015 TCGGACTAGCTAGCTCCCAG 60.179 60.000 23.26 16.05 0.00 4.45
1523 9441 0.179015 CTCGGACTAGCTAGCTCCCA 60.179 60.000 23.26 17.07 0.00 4.37
1524 9442 0.179012 ACTCGGACTAGCTAGCTCCC 60.179 60.000 23.26 19.03 0.00 4.30
1637 9561 3.243941 GCCCTTGTTGTTCCGGTTTTTAT 60.244 43.478 0.00 0.00 0.00 1.40
1638 9562 2.101082 GCCCTTGTTGTTCCGGTTTTTA 59.899 45.455 0.00 0.00 0.00 1.52
1663 9587 1.144093 TGTGTTAGTCTTTGGGGTGGG 59.856 52.381 0.00 0.00 0.00 4.61
1666 9590 2.158667 CCTGTGTGTTAGTCTTTGGGGT 60.159 50.000 0.00 0.00 0.00 4.95
1667 9591 2.504367 CCTGTGTGTTAGTCTTTGGGG 58.496 52.381 0.00 0.00 0.00 4.96
1749 9677 0.522076 GATTTGCAGCTTCGAAGGCG 60.522 55.000 25.77 14.35 39.35 5.52
1963 9891 2.687200 AGGTATGTCAGGGCGGCA 60.687 61.111 12.47 0.00 0.00 5.69
1971 9899 1.327690 GGGCGAGTGGAGGTATGTCA 61.328 60.000 0.00 0.00 0.00 3.58
1998 9926 2.202946 TGTCTTGTGCGGCGTTGA 60.203 55.556 9.37 0.00 0.00 3.18
2048 9976 1.442769 GACATTCGTGGTCTGCATGT 58.557 50.000 0.00 0.00 32.54 3.21
2066 9997 3.463585 GCCCCGGATGTGGTACGA 61.464 66.667 0.73 0.00 35.67 3.43
2106 10037 2.336809 CGTCTCAGATAGGGCGGC 59.663 66.667 0.00 0.00 0.00 6.53
2114 10045 1.356979 CGGTCGATGCGTCTCAGAT 59.643 57.895 4.05 0.00 0.00 2.90
2161 10092 2.685106 TTGGTTGGGTGGCATTCTTA 57.315 45.000 0.00 0.00 0.00 2.10
2213 10145 1.600023 TTTCGGGAACAATGCGAGTT 58.400 45.000 0.00 0.00 0.00 3.01
2236 10168 1.000717 TCTGTTTGTGCGTCGAGATGA 60.001 47.619 0.00 0.00 0.00 2.92
2291 10223 1.890489 TGAATCTCTTTGTCGTCGGGA 59.110 47.619 0.00 0.00 0.00 5.14
2309 10241 5.623141 CGAGTGAATCAAAGAGGTCTCATGA 60.623 44.000 0.00 0.00 34.05 3.07
2310 10242 4.565962 CGAGTGAATCAAAGAGGTCTCATG 59.434 45.833 0.55 0.00 0.00 3.07
2311 10243 4.221703 ACGAGTGAATCAAAGAGGTCTCAT 59.778 41.667 0.00 0.00 0.00 2.90
2312 10244 3.574396 ACGAGTGAATCAAAGAGGTCTCA 59.426 43.478 0.00 0.00 0.00 3.27
2313 10245 4.170256 GACGAGTGAATCAAAGAGGTCTC 58.830 47.826 0.00 0.00 0.00 3.36
2314 10246 3.056465 GGACGAGTGAATCAAAGAGGTCT 60.056 47.826 0.00 0.00 0.00 3.85
2315 10247 3.056465 AGGACGAGTGAATCAAAGAGGTC 60.056 47.826 0.00 0.00 0.00 3.85
2316 10248 2.900546 AGGACGAGTGAATCAAAGAGGT 59.099 45.455 0.00 0.00 0.00 3.85
2335 10267 5.295431 TGATTTACATGAAAGCGTCAAGG 57.705 39.130 0.00 0.00 40.50 3.61
2364 10296 1.817447 AGCAAGATTGGAAAGAGCTGC 59.183 47.619 0.00 0.00 0.00 5.25
2383 10315 5.438761 AAGGGTTCACATTTTTCGAAGAG 57.561 39.130 0.00 0.00 38.43 2.85
2389 10327 7.552458 AACAATGAAAGGGTTCACATTTTTC 57.448 32.000 0.00 0.00 46.40 2.29


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

AutoCloner maintained by Alex Coulton.