Multiple sequence alignment - TraesCS7A01G034000

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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 TraesCS7A01G034000 chr7A 100.000 5229 0 0 1 5229 14898083 14892855 0.000000e+00 9657.0
1 TraesCS7A01G034000 chr7A 81.882 712 126 3 1877 2587 91294607 91295316 9.690000e-167 597.0
2 TraesCS7A01G034000 chr7A 80.764 707 127 9 1887 2588 14821096 14820394 1.280000e-150 544.0
3 TraesCS7A01G034000 chr7A 92.698 315 23 0 1 315 149843339 149843025 6.170000e-124 455.0
4 TraesCS7A01G034000 chr7A 92.628 312 23 0 1 312 712117567 712117878 2.870000e-122 449.0
5 TraesCS7A01G034000 chr7A 77.119 118 25 2 1717 1833 5108995 5109111 3.380000e-07 67.6
6 TraesCS7A01G034000 chr7D 94.014 3291 121 16 782 4064 16061274 16058052 0.000000e+00 4916.0
7 TraesCS7A01G034000 chr7D 92.246 748 44 5 3356 4103 16016218 16015485 0.000000e+00 1048.0
8 TraesCS7A01G034000 chr7D 91.979 748 44 5 3356 4103 16007627 16006896 0.000000e+00 1035.0
9 TraesCS7A01G034000 chr7D 91.845 748 45 7 3356 4103 16019972 16019241 0.000000e+00 1029.0
10 TraesCS7A01G034000 chr7D 90.307 619 45 10 4615 5227 16006146 16005537 0.000000e+00 797.0
11 TraesCS7A01G034000 chr7D 89.644 618 48 10 4615 5227 16057262 16056656 0.000000e+00 773.0
12 TraesCS7A01G034000 chr7D 90.674 579 31 13 4054 4616 16058020 16057449 0.000000e+00 749.0
13 TraesCS7A01G034000 chr7D 90.121 577 40 8 4054 4618 16006900 16006329 0.000000e+00 734.0
14 TraesCS7A01G034000 chr7D 89.860 572 41 10 4058 4618 16019241 16018676 0.000000e+00 719.0
15 TraesCS7A01G034000 chr7D 94.105 475 18 5 313 783 16062192 16061724 0.000000e+00 713.0
16 TraesCS7A01G034000 chr7D 89.510 572 43 10 4058 4618 16015485 16014920 0.000000e+00 708.0
17 TraesCS7A01G034000 chr7D 90.656 503 33 9 4731 5227 15941913 15941419 0.000000e+00 656.0
18 TraesCS7A01G034000 chr7D 80.664 693 124 10 1901 2588 15912935 15912248 3.590000e-146 529.0
19 TraesCS7A01G034000 chr7D 76.747 916 188 20 1886 2783 15920411 15919503 6.090000e-134 488.0
20 TraesCS7A01G034000 chr3D 92.174 2594 103 30 2073 4616 584823548 584826091 0.000000e+00 3574.0
21 TraesCS7A01G034000 chr3D 94.308 1300 50 5 779 2077 584817104 584818380 0.000000e+00 1969.0
22 TraesCS7A01G034000 chr3D 90.307 619 42 12 4615 5227 584826278 584826884 0.000000e+00 795.0
23 TraesCS7A01G034000 chr3D 95.085 468 16 4 313 780 584816189 584816649 0.000000e+00 730.0
24 TraesCS7A01G034000 chr3D 79.745 706 133 10 1888 2588 584932134 584932834 2.170000e-138 503.0
25 TraesCS7A01G034000 chr3D 76.500 400 82 9 2372 2762 584888863 584889259 1.910000e-49 207.0
26 TraesCS7A01G034000 chr7B 94.447 2143 98 8 1406 3540 711433939 711431810 0.000000e+00 3278.0
27 TraesCS7A01G034000 chr7B 91.410 617 49 4 782 1396 711434601 711433987 0.000000e+00 843.0
28 TraesCS7A01G034000 chr7B 79.260 622 78 30 4615 5222 711430564 711429980 2.280000e-103 387.0
29 TraesCS7A01G034000 chr7B 77.922 539 80 23 4093 4615 711431257 711430742 3.060000e-77 300.0
30 TraesCS7A01G034000 chr7B 91.045 201 15 1 3562 3759 711431688 711431488 8.630000e-68 268.0
31 TraesCS7A01G034000 chr7B 82.400 125 14 2 659 783 711434893 711434777 9.260000e-18 102.0
32 TraesCS7A01G034000 chr4A 92.641 2215 130 14 1430 3633 718967831 718970023 0.000000e+00 3157.0
33 TraesCS7A01G034000 chr4A 92.641 2215 130 14 1430 3633 718980078 718982270 0.000000e+00 3157.0
34 TraesCS7A01G034000 chr4A 92.628 312 22 1 1 312 585618652 585618342 1.030000e-121 448.0
35 TraesCS7A01G034000 chr4A 81.356 118 16 3 3107 3219 719121040 719121156 2.010000e-14 91.6
36 TraesCS7A01G034000 chrUn 92.758 718 39 4 3347 4064 457338120 457338824 0.000000e+00 1026.0
37 TraesCS7A01G034000 chrUn 94.026 385 13 1 3356 3740 462295653 462295279 4.540000e-160 575.0
38 TraesCS7A01G034000 chrUn 93.243 148 9 1 4054 4200 457338856 457339003 3.170000e-52 217.0
39 TraesCS7A01G034000 chr5A 93.038 316 21 1 1 316 666238535 666238221 1.330000e-125 460.0
40 TraesCS7A01G034000 chr5A 92.949 312 21 1 1 312 670276384 670276074 2.220000e-123 453.0
41 TraesCS7A01G034000 chr6A 92.308 312 24 0 1 312 279843047 279843358 1.340000e-120 444.0
42 TraesCS7A01G034000 chr3A 92.038 314 25 0 1 314 674764848 674765161 4.810000e-120 442.0
43 TraesCS7A01G034000 chr3A 97.059 34 1 0 4363 4396 717489952 717489985 2.030000e-04 58.4
44 TraesCS7A01G034000 chr2A 91.987 312 25 0 1 312 293853915 293854226 6.220000e-119 438.0
45 TraesCS7A01G034000 chr1A 92.233 309 24 0 1 309 4800375 4800683 6.220000e-119 438.0


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 TraesCS7A01G034000 chr7A 14892855 14898083 5228 True 9657.000000 9657 100.000000 1 5229 1 chr7A.!!$R2 5228
1 TraesCS7A01G034000 chr7A 91294607 91295316 709 False 597.000000 597 81.882000 1877 2587 1 chr7A.!!$F2 710
2 TraesCS7A01G034000 chr7A 14820394 14821096 702 True 544.000000 544 80.764000 1887 2588 1 chr7A.!!$R1 701
3 TraesCS7A01G034000 chr7D 16056656 16062192 5536 True 1787.750000 4916 92.109250 313 5227 4 chr7D.!!$R6 4914
4 TraesCS7A01G034000 chr7D 16014920 16019972 5052 True 876.000000 1048 90.865250 3356 4618 4 chr7D.!!$R5 1262
5 TraesCS7A01G034000 chr7D 16005537 16007627 2090 True 855.333333 1035 90.802333 3356 5227 3 chr7D.!!$R4 1871
6 TraesCS7A01G034000 chr7D 15912248 15912935 687 True 529.000000 529 80.664000 1901 2588 1 chr7D.!!$R1 687
7 TraesCS7A01G034000 chr7D 15919503 15920411 908 True 488.000000 488 76.747000 1886 2783 1 chr7D.!!$R2 897
8 TraesCS7A01G034000 chr3D 584823548 584826884 3336 False 2184.500000 3574 91.240500 2073 5227 2 chr3D.!!$F4 3154
9 TraesCS7A01G034000 chr3D 584816189 584818380 2191 False 1349.500000 1969 94.696500 313 2077 2 chr3D.!!$F3 1764
10 TraesCS7A01G034000 chr3D 584932134 584932834 700 False 503.000000 503 79.745000 1888 2588 1 chr3D.!!$F2 700
11 TraesCS7A01G034000 chr7B 711429980 711434893 4913 True 863.000000 3278 86.080667 659 5222 6 chr7B.!!$R1 4563
12 TraesCS7A01G034000 chr4A 718967831 718970023 2192 False 3157.000000 3157 92.641000 1430 3633 1 chr4A.!!$F1 2203
13 TraesCS7A01G034000 chr4A 718980078 718982270 2192 False 3157.000000 3157 92.641000 1430 3633 1 chr4A.!!$F2 2203
14 TraesCS7A01G034000 chrUn 457338120 457339003 883 False 621.500000 1026 93.000500 3347 4200 2 chrUn.!!$F1 853

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
94 95 0.026674 CGGACGCTGCACATTACATG 59.973 55.000 0.00 0.0 0.00 3.21 F
238 239 0.032540 GCTGCACAAAAAGGTCAGGG 59.967 55.000 0.00 0.0 0.00 4.45 F
240 241 0.032615 TGCACAAAAAGGTCAGGGGT 60.033 50.000 0.00 0.0 0.00 4.95 F
241 242 0.389025 GCACAAAAAGGTCAGGGGTG 59.611 55.000 0.00 0.0 0.00 4.61 F
646 651 0.463295 CATCGATCAGCAGCCCAAGT 60.463 55.000 0.00 0.0 0.00 3.16 F
1295 1770 0.887247 TGCACGGATGTTGGATTTGG 59.113 50.000 0.00 0.0 0.00 3.28 F
2971 3510 1.624813 CAATGGGTTTCTGCCATTGGT 59.375 47.619 5.49 0.0 43.81 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 2284 0.980423 GGCTAGCATTAGGAGGGGAG 59.020 60.000 18.24 0.00 0.00 4.30 R
2543 3075 2.490903 AGCTCAAGTGCAATCCAATGTC 59.509 45.455 0.00 0.00 34.99 3.06 R
2682 3220 9.535878 GCTTCAATATAAGATATAGTAGCCACC 57.464 37.037 0.00 0.00 0.00 4.61 R
2905 3444 2.979814 TCACTACATGCGCATTACCT 57.020 45.000 22.81 6.00 0.00 3.08 R
3084 3623 1.664874 GGACGTTGGCAATTTCCGTTC 60.665 52.381 13.67 8.96 0.00 3.95 R
3568 4217 0.316204 GGCACAAGCAGCAATGTTCT 59.684 50.000 0.00 0.00 44.61 3.01 R
5076 9762 0.034767 ATCCCTCGACGGTACTGTCA 60.035 55.000 29.50 17.62 38.84 3.58 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
17 18 3.814906 TGGTGTGTGTGGGGTGGG 61.815 66.667 0.00 0.00 0.00 4.61
18 19 4.596585 GGTGTGTGTGGGGTGGGG 62.597 72.222 0.00 0.00 0.00 4.96
19 20 4.596585 GTGTGTGTGGGGTGGGGG 62.597 72.222 0.00 0.00 0.00 5.40
56 57 2.682893 CAGCCGCTGGATAAGTCAC 58.317 57.895 12.93 0.00 0.00 3.67
57 58 0.108186 CAGCCGCTGGATAAGTCACA 60.108 55.000 12.93 0.00 0.00 3.58
58 59 0.176680 AGCCGCTGGATAAGTCACAG 59.823 55.000 0.00 0.00 35.40 3.66
59 60 0.108138 GCCGCTGGATAAGTCACAGT 60.108 55.000 0.00 0.00 34.79 3.55
60 61 1.645034 CCGCTGGATAAGTCACAGTG 58.355 55.000 0.00 0.00 41.18 3.66
61 62 1.002366 CGCTGGATAAGTCACAGTGC 58.998 55.000 0.00 0.00 36.16 4.40
62 63 1.672737 CGCTGGATAAGTCACAGTGCA 60.673 52.381 0.00 0.00 36.16 4.57
63 64 2.426522 GCTGGATAAGTCACAGTGCAA 58.573 47.619 0.00 0.00 34.79 4.08
64 65 2.160417 GCTGGATAAGTCACAGTGCAAC 59.840 50.000 0.00 0.00 34.79 4.17
65 66 2.412870 TGGATAAGTCACAGTGCAACG 58.587 47.619 0.00 0.00 45.86 4.10
66 67 1.128692 GGATAAGTCACAGTGCAACGC 59.871 52.381 0.00 0.00 45.86 4.84
67 68 1.128692 GATAAGTCACAGTGCAACGCC 59.871 52.381 0.00 0.00 45.86 5.68
68 69 0.105964 TAAGTCACAGTGCAACGCCT 59.894 50.000 0.00 0.00 45.86 5.52
69 70 0.105964 AAGTCACAGTGCAACGCCTA 59.894 50.000 0.00 0.00 45.86 3.93
70 71 0.600255 AGTCACAGTGCAACGCCTAC 60.600 55.000 0.00 0.00 45.86 3.18
71 72 1.663388 TCACAGTGCAACGCCTACG 60.663 57.895 0.00 0.00 45.86 3.51
72 73 2.357034 ACAGTGCAACGCCTACGG 60.357 61.111 0.00 0.00 45.86 4.02
73 74 3.118454 CAGTGCAACGCCTACGGG 61.118 66.667 0.00 0.00 45.86 5.28
90 91 2.817834 GCCGGACGCTGCACATTA 60.818 61.111 5.05 0.00 0.00 1.90
91 92 3.089784 CCGGACGCTGCACATTAC 58.910 61.111 0.00 0.00 0.00 1.89
92 93 1.739929 CCGGACGCTGCACATTACA 60.740 57.895 0.00 0.00 0.00 2.41
93 94 1.089481 CCGGACGCTGCACATTACAT 61.089 55.000 0.00 0.00 0.00 2.29
94 95 0.026674 CGGACGCTGCACATTACATG 59.973 55.000 0.00 0.00 0.00 3.21
95 96 1.086696 GGACGCTGCACATTACATGT 58.913 50.000 2.69 2.69 46.22 3.21
103 104 2.179764 ACATTACATGTGTGGCGCC 58.820 52.632 22.73 22.73 43.01 6.53
104 105 0.322456 ACATTACATGTGTGGCGCCT 60.322 50.000 29.70 7.80 43.01 5.52
105 106 1.065782 ACATTACATGTGTGGCGCCTA 60.066 47.619 29.70 14.39 43.01 3.93
106 107 1.599071 CATTACATGTGTGGCGCCTAG 59.401 52.381 29.70 12.91 0.00 3.02
119 120 4.277593 CCTAGCTCGGAGGCGCTG 62.278 72.222 7.64 0.00 36.29 5.18
120 121 4.940593 CTAGCTCGGAGGCGCTGC 62.941 72.222 7.64 0.00 36.29 5.25
160 161 4.314440 GCTGCCACGGTGGACTGA 62.314 66.667 30.65 9.58 40.96 3.41
161 162 2.425592 CTGCCACGGTGGACTGAA 59.574 61.111 30.65 8.78 40.96 3.02
162 163 1.669115 CTGCCACGGTGGACTGAAG 60.669 63.158 30.65 14.13 40.96 3.02
163 164 2.383245 CTGCCACGGTGGACTGAAGT 62.383 60.000 30.65 0.00 40.96 3.01
164 165 1.961277 GCCACGGTGGACTGAAGTG 60.961 63.158 30.65 1.03 40.96 3.16
165 166 1.961277 CCACGGTGGACTGAAGTGC 60.961 63.158 22.77 0.00 40.96 4.40
166 167 1.227527 CACGGTGGACTGAAGTGCA 60.228 57.895 0.00 0.00 44.12 4.57
170 171 3.731136 TGGACTGAAGTGCAACGC 58.269 55.556 1.78 0.00 43.38 4.84
171 172 1.891919 TGGACTGAAGTGCAACGCC 60.892 57.895 1.78 0.00 43.38 5.68
172 173 2.617274 GGACTGAAGTGCAACGCCC 61.617 63.158 0.00 0.00 45.86 6.13
173 174 2.594592 ACTGAAGTGCAACGCCCC 60.595 61.111 0.00 0.00 45.86 5.80
174 175 3.365265 CTGAAGTGCAACGCCCCC 61.365 66.667 0.00 0.00 45.86 5.40
182 183 4.530857 CAACGCCCCCGAGCTAGG 62.531 72.222 5.78 5.78 38.29 3.02
194 195 4.508128 GCTAGGCGCTGCACCGTA 62.508 66.667 7.64 0.00 35.14 4.02
195 196 2.278857 CTAGGCGCTGCACCGTAG 60.279 66.667 7.64 2.34 0.00 3.51
230 231 4.940593 GCGGGCGCTGCACAAAAA 62.941 61.111 18.05 0.00 35.55 1.94
231 232 2.730604 CGGGCGCTGCACAAAAAG 60.731 61.111 7.64 0.00 0.00 2.27
232 233 2.356194 GGGCGCTGCACAAAAAGG 60.356 61.111 7.64 0.00 0.00 3.11
233 234 2.417097 GGCGCTGCACAAAAAGGT 59.583 55.556 7.64 0.00 0.00 3.50
234 235 1.661509 GGCGCTGCACAAAAAGGTC 60.662 57.895 7.64 0.00 0.00 3.85
235 236 1.065600 GCGCTGCACAAAAAGGTCA 59.934 52.632 0.00 0.00 0.00 4.02
236 237 0.936297 GCGCTGCACAAAAAGGTCAG 60.936 55.000 0.00 0.00 0.00 3.51
237 238 0.318107 CGCTGCACAAAAAGGTCAGG 60.318 55.000 0.00 0.00 0.00 3.86
238 239 0.032540 GCTGCACAAAAAGGTCAGGG 59.967 55.000 0.00 0.00 0.00 4.45
239 240 0.675633 CTGCACAAAAAGGTCAGGGG 59.324 55.000 0.00 0.00 0.00 4.79
240 241 0.032615 TGCACAAAAAGGTCAGGGGT 60.033 50.000 0.00 0.00 0.00 4.95
241 242 0.389025 GCACAAAAAGGTCAGGGGTG 59.611 55.000 0.00 0.00 0.00 4.61
242 243 1.775385 CACAAAAAGGTCAGGGGTGT 58.225 50.000 0.00 0.00 0.00 4.16
243 244 1.408702 CACAAAAAGGTCAGGGGTGTG 59.591 52.381 0.00 0.00 0.00 3.82
244 245 1.286553 ACAAAAAGGTCAGGGGTGTGA 59.713 47.619 0.00 0.00 0.00 3.58
245 246 2.291930 ACAAAAAGGTCAGGGGTGTGAA 60.292 45.455 0.00 0.00 0.00 3.18
246 247 2.763448 CAAAAAGGTCAGGGGTGTGAAA 59.237 45.455 0.00 0.00 0.00 2.69
247 248 3.328535 AAAAGGTCAGGGGTGTGAAAT 57.671 42.857 0.00 0.00 0.00 2.17
248 249 4.463050 AAAAGGTCAGGGGTGTGAAATA 57.537 40.909 0.00 0.00 0.00 1.40
249 250 3.721087 AAGGTCAGGGGTGTGAAATAG 57.279 47.619 0.00 0.00 0.00 1.73
250 251 2.632537 AGGTCAGGGGTGTGAAATAGT 58.367 47.619 0.00 0.00 0.00 2.12
251 252 2.986728 AGGTCAGGGGTGTGAAATAGTT 59.013 45.455 0.00 0.00 0.00 2.24
252 253 3.397955 AGGTCAGGGGTGTGAAATAGTTT 59.602 43.478 0.00 0.00 0.00 2.66
253 254 4.141018 AGGTCAGGGGTGTGAAATAGTTTT 60.141 41.667 0.00 0.00 0.00 2.43
254 255 5.073965 AGGTCAGGGGTGTGAAATAGTTTTA 59.926 40.000 0.00 0.00 0.00 1.52
255 256 5.182570 GGTCAGGGGTGTGAAATAGTTTTAC 59.817 44.000 0.00 0.00 0.00 2.01
256 257 4.998672 TCAGGGGTGTGAAATAGTTTTACG 59.001 41.667 0.00 0.00 32.37 3.18
257 258 4.155280 CAGGGGTGTGAAATAGTTTTACGG 59.845 45.833 0.00 0.00 32.37 4.02
258 259 3.441222 GGGGTGTGAAATAGTTTTACGGG 59.559 47.826 0.00 0.00 32.37 5.28
259 260 3.119743 GGGTGTGAAATAGTTTTACGGGC 60.120 47.826 0.00 0.00 32.37 6.13
260 261 3.502979 GGTGTGAAATAGTTTTACGGGCA 59.497 43.478 0.00 0.00 32.37 5.36
261 262 4.379082 GGTGTGAAATAGTTTTACGGGCAG 60.379 45.833 0.00 0.00 32.37 4.85
262 263 4.214758 GTGTGAAATAGTTTTACGGGCAGT 59.785 41.667 0.00 0.00 32.37 4.40
263 264 4.822896 TGTGAAATAGTTTTACGGGCAGTT 59.177 37.500 0.00 0.00 32.37 3.16
264 265 5.049267 TGTGAAATAGTTTTACGGGCAGTTC 60.049 40.000 0.00 0.00 32.37 3.01
265 266 5.049267 GTGAAATAGTTTTACGGGCAGTTCA 60.049 40.000 0.00 0.00 0.00 3.18
266 267 5.708230 TGAAATAGTTTTACGGGCAGTTCAT 59.292 36.000 0.00 0.00 0.00 2.57
267 268 6.207810 TGAAATAGTTTTACGGGCAGTTCATT 59.792 34.615 0.00 0.00 0.00 2.57
268 269 5.813080 ATAGTTTTACGGGCAGTTCATTC 57.187 39.130 0.00 0.00 0.00 2.67
269 270 2.817844 AGTTTTACGGGCAGTTCATTCC 59.182 45.455 0.00 0.00 0.00 3.01
270 271 1.444836 TTTACGGGCAGTTCATTCCG 58.555 50.000 0.00 0.00 46.95 4.30
272 273 3.177600 CGGGCAGTTCATTCCGTG 58.822 61.111 0.00 0.00 37.92 4.94
273 274 1.375396 CGGGCAGTTCATTCCGTGA 60.375 57.895 0.00 0.00 37.92 4.35
274 275 0.953471 CGGGCAGTTCATTCCGTGAA 60.953 55.000 0.00 0.00 44.36 3.18
284 285 5.621197 TTCATTCCGTGAATTGATTTCGT 57.379 34.783 0.00 0.00 41.79 3.85
285 286 5.216566 TCATTCCGTGAATTGATTTCGTC 57.783 39.130 0.00 0.00 37.13 4.20
286 287 4.094294 TCATTCCGTGAATTGATTTCGTCC 59.906 41.667 0.00 0.00 37.13 4.79
287 288 2.352388 TCCGTGAATTGATTTCGTCCC 58.648 47.619 0.00 0.00 37.13 4.46
288 289 2.080693 CCGTGAATTGATTTCGTCCCA 58.919 47.619 0.00 0.00 37.13 4.37
289 290 2.486203 CCGTGAATTGATTTCGTCCCAA 59.514 45.455 0.00 0.00 37.13 4.12
290 291 3.426159 CCGTGAATTGATTTCGTCCCAAG 60.426 47.826 0.00 0.00 37.13 3.61
291 292 3.426159 CGTGAATTGATTTCGTCCCAAGG 60.426 47.826 0.00 0.00 37.13 3.61
292 293 3.506067 GTGAATTGATTTCGTCCCAAGGT 59.494 43.478 0.00 0.00 37.13 3.50
293 294 3.756434 TGAATTGATTTCGTCCCAAGGTC 59.244 43.478 0.00 0.00 37.13 3.85
294 295 2.940994 TTGATTTCGTCCCAAGGTCA 57.059 45.000 0.00 0.00 0.00 4.02
295 296 2.940994 TGATTTCGTCCCAAGGTCAA 57.059 45.000 0.00 0.00 0.00 3.18
296 297 3.216187 TGATTTCGTCCCAAGGTCAAA 57.784 42.857 0.00 0.00 0.00 2.69
297 298 3.556999 TGATTTCGTCCCAAGGTCAAAA 58.443 40.909 0.00 0.00 0.00 2.44
298 299 4.148838 TGATTTCGTCCCAAGGTCAAAAT 58.851 39.130 0.00 0.00 0.00 1.82
299 300 4.586841 TGATTTCGTCCCAAGGTCAAAATT 59.413 37.500 0.00 0.00 0.00 1.82
300 301 4.314740 TTTCGTCCCAAGGTCAAAATTG 57.685 40.909 0.00 0.00 0.00 2.32
301 302 2.938838 TCGTCCCAAGGTCAAAATTGT 58.061 42.857 0.00 0.00 0.00 2.71
302 303 2.882137 TCGTCCCAAGGTCAAAATTGTC 59.118 45.455 0.00 0.00 0.00 3.18
303 304 2.621055 CGTCCCAAGGTCAAAATTGTCA 59.379 45.455 0.00 0.00 0.00 3.58
304 305 3.067461 CGTCCCAAGGTCAAAATTGTCAA 59.933 43.478 0.00 0.00 0.00 3.18
305 306 4.440802 CGTCCCAAGGTCAAAATTGTCAAA 60.441 41.667 0.00 0.00 0.00 2.69
306 307 5.610398 GTCCCAAGGTCAAAATTGTCAAAT 58.390 37.500 0.00 0.00 0.00 2.32
307 308 6.054941 GTCCCAAGGTCAAAATTGTCAAATT 58.945 36.000 0.00 0.00 37.61 1.82
308 309 6.542005 GTCCCAAGGTCAAAATTGTCAAATTT 59.458 34.615 0.00 0.00 45.81 1.82
309 310 6.541641 TCCCAAGGTCAAAATTGTCAAATTTG 59.458 34.615 16.75 16.75 43.63 2.32
310 311 6.200808 CCAAGGTCAAAATTGTCAAATTTGC 58.799 36.000 17.69 13.41 43.63 3.68
311 312 6.200808 CAAGGTCAAAATTGTCAAATTTGCC 58.799 36.000 17.69 19.32 43.63 4.52
345 346 2.159627 CACACGCATTTGAACCCTAGTC 59.840 50.000 0.00 0.00 0.00 2.59
541 546 6.183360 TGGATAAATTTGTATGGCTCGGAAAC 60.183 38.462 0.00 0.00 0.00 2.78
581 586 0.856982 ATTTGGGTTGGGTGGAGACA 59.143 50.000 0.00 0.00 38.70 3.41
589 594 2.341846 TGGGTGGAGACAGAAACAAC 57.658 50.000 0.00 0.00 44.46 3.32
646 651 0.463295 CATCGATCAGCAGCCCAAGT 60.463 55.000 0.00 0.00 0.00 3.16
654 659 2.341176 CAGCCCAAGTGCAAAGCC 59.659 61.111 0.00 0.00 0.00 4.35
696 701 3.123804 CAGTATAACGCCATGTCCTGTC 58.876 50.000 0.00 0.00 0.00 3.51
699 704 2.161078 TAACGCCATGTCCTGTCGCA 62.161 55.000 0.00 0.00 0.00 5.10
730 735 8.778358 CAGTAGATTAATTAGGATGAGCCAAAC 58.222 37.037 0.00 0.00 40.02 2.93
731 736 8.718656 AGTAGATTAATTAGGATGAGCCAAACT 58.281 33.333 0.00 0.00 40.02 2.66
736 743 2.270434 AGGATGAGCCAAACTAGGGA 57.730 50.000 0.00 0.00 40.02 4.20
737 744 2.781667 AGGATGAGCCAAACTAGGGAT 58.218 47.619 0.00 0.00 40.02 3.85
738 745 3.941629 AGGATGAGCCAAACTAGGGATA 58.058 45.455 0.00 0.00 40.02 2.59
739 746 3.906846 AGGATGAGCCAAACTAGGGATAG 59.093 47.826 0.00 0.00 40.02 2.08
740 747 3.904339 GGATGAGCCAAACTAGGGATAGA 59.096 47.826 0.00 0.00 36.34 1.98
741 748 4.348168 GGATGAGCCAAACTAGGGATAGAA 59.652 45.833 0.00 0.00 36.34 2.10
742 749 5.013599 GGATGAGCCAAACTAGGGATAGAAT 59.986 44.000 0.00 0.00 36.34 2.40
743 750 5.552870 TGAGCCAAACTAGGGATAGAATC 57.447 43.478 0.00 0.00 0.00 2.52
817 1290 1.300620 CTCTGCCACCGTTTGTCGA 60.301 57.895 0.00 0.00 42.86 4.20
848 1321 5.649782 AAAGATTTAACTGCATGGAGGTG 57.350 39.130 16.00 0.00 0.00 4.00
856 1329 1.538512 CTGCATGGAGGTGTTTGACTG 59.461 52.381 6.28 0.00 0.00 3.51
1047 1521 4.156556 TGAGTGTTCAATGATTTGGCTAGC 59.843 41.667 6.04 6.04 33.44 3.42
1063 1537 1.556911 CTAGCTGTGGTCCTTGTGGAT 59.443 52.381 0.00 0.00 45.29 3.41
1130 1604 8.604184 AGATAGCCAATACATCATTCTCATTCT 58.396 33.333 0.00 0.00 0.00 2.40
1183 1657 8.443160 ACACTTACATGTGATCGAAATTACTTG 58.557 33.333 9.11 0.00 40.12 3.16
1192 1666 1.470098 CGAAATTACTTGCAGCTGCCT 59.530 47.619 34.64 19.52 41.18 4.75
1232 1706 3.696548 GCTTGAACCCTTAAAGCTGCTAT 59.303 43.478 0.90 0.00 42.40 2.97
1292 1767 1.167851 CACTGCACGGATGTTGGATT 58.832 50.000 0.00 0.00 0.00 3.01
1295 1770 0.887247 TGCACGGATGTTGGATTTGG 59.113 50.000 0.00 0.00 0.00 3.28
1380 1855 8.405531 TGCAGGTTTATTGCACTATTAGAATTC 58.594 33.333 0.00 0.00 45.89 2.17
1752 2278 3.251484 TCTCCTTCTCCAACCTGATGTT 58.749 45.455 0.00 0.00 37.80 2.71
1758 2284 4.021102 TCTCCAACCTGATGTTTCTTCC 57.979 45.455 0.00 0.00 34.00 3.46
1842 2368 5.824624 CACAGATATAGCCAAAGTCAACCAT 59.175 40.000 0.00 0.00 0.00 3.55
2274 2806 4.676546 TCGAGTCAAGCATGATCAGTAAG 58.323 43.478 0.09 0.00 38.01 2.34
2543 3075 4.679373 ACTGCTATAACCATGAGTCTGG 57.321 45.455 0.00 6.98 42.35 3.86
2612 3150 2.723124 ATTTTCATGGGTTGTGACGC 57.277 45.000 0.00 0.00 39.05 5.19
2682 3220 8.044908 TGTAGGTGATTATGATGATCATGATGG 58.955 37.037 16.20 0.00 37.70 3.51
2739 3277 8.345565 CCTATTATTGCAAGGATGTGTAAGAAC 58.654 37.037 4.94 0.00 29.19 3.01
2769 3308 3.311106 GTTTGGTAGTTGTCGATCGTCA 58.689 45.455 15.94 13.37 0.00 4.35
2905 3444 6.912051 GCATTCATCGTGATGTTGCTAATTTA 59.088 34.615 21.86 0.00 41.34 1.40
2926 3465 3.198068 AGGTAATGCGCATGTAGTGAAG 58.802 45.455 26.09 0.00 0.00 3.02
2971 3510 1.624813 CAATGGGTTTCTGCCATTGGT 59.375 47.619 5.49 0.00 43.81 3.67
2972 3511 2.028561 ATGGGTTTCTGCCATTGGTT 57.971 45.000 4.26 0.00 0.00 3.67
2973 3512 1.799933 TGGGTTTCTGCCATTGGTTT 58.200 45.000 4.26 0.00 0.00 3.27
2974 3513 2.122768 TGGGTTTCTGCCATTGGTTTT 58.877 42.857 4.26 0.00 0.00 2.43
2975 3514 2.158842 TGGGTTTCTGCCATTGGTTTTG 60.159 45.455 4.26 0.00 0.00 2.44
2976 3515 1.872952 GGTTTCTGCCATTGGTTTTGC 59.127 47.619 4.26 0.00 0.00 3.68
2977 3516 2.559440 GTTTCTGCCATTGGTTTTGCA 58.441 42.857 4.26 0.00 0.00 4.08
3033 3572 7.214381 GGGTTTCCTGTTATTGTTTAAGCTTT 58.786 34.615 3.20 0.00 0.00 3.51
3084 3623 7.278646 GCAAGGCTTTATATTTCCTTTTTCTGG 59.721 37.037 0.00 0.00 36.85 3.86
3771 4423 4.631813 ACGACAACTCCATAGAAATCTTGC 59.368 41.667 0.00 0.00 0.00 4.01
3782 4434 4.236527 AGAAATCTTGCGATAAAGGGGT 57.763 40.909 0.00 0.00 0.00 4.95
3796 4448 7.600960 CGATAAAGGGGTATTCCTACTTCTAC 58.399 42.308 0.85 0.00 35.80 2.59
3812 4464 6.650427 ACTTCTACCAATTTCCTGGAAAAC 57.350 37.500 24.44 0.00 38.96 2.43
3826 4490 3.760684 CTGGAAAACAATTGAGAGAGGGG 59.239 47.826 13.59 0.00 0.00 4.79
3827 4491 3.397618 TGGAAAACAATTGAGAGAGGGGA 59.602 43.478 13.59 0.00 0.00 4.81
3849 4513 0.104671 GGAGAGAGATCCTGCAGTGC 59.895 60.000 13.81 8.58 36.35 4.40
4031 8453 5.065218 ACGCAATGTAAAATTTTGTTTGCCA 59.935 32.000 25.26 11.57 35.71 4.92
4174 8643 6.823531 TGATCCGGCGTTTAAAAATATATCG 58.176 36.000 6.01 0.00 0.00 2.92
4551 9040 4.495459 AACCAATAGGGAAAGGGGAAAA 57.505 40.909 0.00 0.00 41.15 2.29
4589 9079 5.924356 ACCCAAAAATTCCGATGAAAAACT 58.076 33.333 0.00 0.00 33.32 2.66
4649 9329 0.958822 GGTAGTTTTGGCCCACACTG 59.041 55.000 5.90 0.00 0.00 3.66
4650 9330 1.687563 GTAGTTTTGGCCCACACTGT 58.312 50.000 5.90 0.00 0.00 3.55
4653 9333 2.028876 AGTTTTGGCCCACACTGTAAC 58.971 47.619 0.00 0.00 0.00 2.50
4657 9337 0.476338 TGGCCCACACTGTAACATGT 59.524 50.000 0.00 0.00 0.00 3.21
4669 9349 1.737236 GTAACATGTTGCATGGCGAGA 59.263 47.619 21.42 0.00 0.00 4.04
4690 9370 0.747255 TAGCGAGTGAATGAGGCTCC 59.253 55.000 12.86 0.00 35.28 4.70
4895 9579 1.740296 GGAGGTGTGTTGCGCGTAT 60.740 57.895 8.43 0.00 0.00 3.06
4900 9584 1.352114 GTGTGTTGCGCGTATTAGGA 58.648 50.000 8.43 0.00 0.00 2.94
4901 9585 1.323534 GTGTGTTGCGCGTATTAGGAG 59.676 52.381 8.43 0.00 0.00 3.69
4902 9586 0.300789 GTGTTGCGCGTATTAGGAGC 59.699 55.000 8.43 5.32 0.00 4.70
4903 9587 0.108567 TGTTGCGCGTATTAGGAGCA 60.109 50.000 8.43 10.16 37.04 4.26
4999 9685 1.612442 ACCGTAGTGGGGAGCACAT 60.612 57.895 0.00 0.00 44.64 3.21
5011 9697 2.135933 GGAGCACATAGTGTATTCCGC 58.864 52.381 0.00 0.00 35.75 5.54
5025 9711 0.322322 TTCCGCGGGAACATAAGTGT 59.678 50.000 27.83 0.00 36.71 3.55
5033 9719 5.506151 CGCGGGAACATAAGTGTAGTACATA 60.506 44.000 6.21 0.00 37.67 2.29
5064 9750 2.930040 CACAAAGTGCACTACTATCGGG 59.070 50.000 22.01 2.34 39.18 5.14
5076 9762 0.107848 CTATCGGGGTTTTCGTGCCT 60.108 55.000 0.00 0.00 0.00 4.75
5095 9781 0.034767 TGACAGTACCGTCGAGGGAT 60.035 55.000 29.83 16.14 46.96 3.85
5127 9814 1.303561 GGAGGGCAAGCACACATGA 60.304 57.895 0.00 0.00 0.00 3.07
5132 9819 3.368248 AGGGCAAGCACACATGAATTAT 58.632 40.909 0.00 0.00 0.00 1.28
5133 9820 3.131577 AGGGCAAGCACACATGAATTATG 59.868 43.478 0.00 0.00 42.68 1.90
5134 9821 2.861935 GGCAAGCACACATGAATTATGC 59.138 45.455 0.00 2.69 40.59 3.14
5167 9858 3.803340 AGAGAGGATTTACCCAGGTTCA 58.197 45.455 0.00 0.00 40.05 3.18
5176 9867 0.178873 ACCCAGGTTCAGGCCTTCTA 60.179 55.000 0.00 0.00 36.58 2.10
5177 9868 0.543749 CCCAGGTTCAGGCCTTCTAG 59.456 60.000 0.00 0.00 36.58 2.43
5178 9869 0.107459 CCAGGTTCAGGCCTTCTAGC 60.107 60.000 0.00 0.27 36.58 3.42
5219 9910 0.382515 CCAGCCTCTAGTGCGTCTAC 59.617 60.000 0.00 0.00 0.00 2.59
5227 9918 1.740585 CTAGTGCGTCTACTGCTCTGT 59.259 52.381 9.90 0.00 36.87 3.41
5228 9919 0.962489 AGTGCGTCTACTGCTCTGTT 59.038 50.000 0.00 0.00 35.09 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.596585 CCCCACCCCACACACACC 62.597 72.222 0.00 0.00 0.00 4.16
2 3 4.596585 CCCCCACCCCACACACAC 62.597 72.222 0.00 0.00 0.00 3.82
38 39 0.108186 TGTGACTTATCCAGCGGCTG 60.108 55.000 22.84 22.84 0.00 4.85
39 40 0.176680 CTGTGACTTATCCAGCGGCT 59.823 55.000 0.00 0.00 0.00 5.52
40 41 0.108138 ACTGTGACTTATCCAGCGGC 60.108 55.000 0.00 0.00 30.41 6.53
41 42 1.645034 CACTGTGACTTATCCAGCGG 58.355 55.000 0.32 0.00 30.41 5.52
42 43 1.002366 GCACTGTGACTTATCCAGCG 58.998 55.000 12.86 0.00 30.41 5.18
43 44 2.099141 TGCACTGTGACTTATCCAGC 57.901 50.000 12.86 0.00 30.41 4.85
44 45 2.413112 CGTTGCACTGTGACTTATCCAG 59.587 50.000 12.86 0.00 32.42 3.86
45 46 2.412870 CGTTGCACTGTGACTTATCCA 58.587 47.619 12.86 0.00 0.00 3.41
46 47 1.128692 GCGTTGCACTGTGACTTATCC 59.871 52.381 12.86 0.00 0.00 2.59
47 48 1.128692 GGCGTTGCACTGTGACTTATC 59.871 52.381 12.86 0.00 0.00 1.75
48 49 1.156736 GGCGTTGCACTGTGACTTAT 58.843 50.000 12.86 0.00 0.00 1.73
49 50 0.105964 AGGCGTTGCACTGTGACTTA 59.894 50.000 12.86 0.00 0.00 2.24
50 51 0.105964 TAGGCGTTGCACTGTGACTT 59.894 50.000 12.86 0.00 0.00 3.01
51 52 0.600255 GTAGGCGTTGCACTGTGACT 60.600 55.000 12.86 0.00 0.00 3.41
52 53 1.860078 GTAGGCGTTGCACTGTGAC 59.140 57.895 12.86 3.63 0.00 3.67
53 54 1.663388 CGTAGGCGTTGCACTGTGA 60.663 57.895 12.86 0.00 0.00 3.58
54 55 2.667318 CCGTAGGCGTTGCACTGTG 61.667 63.158 2.76 2.76 46.14 3.66
55 56 2.357034 CCGTAGGCGTTGCACTGT 60.357 61.111 0.00 0.00 46.14 3.55
73 74 2.817834 TAATGTGCAGCGTCCGGC 60.818 61.111 0.00 0.00 44.05 6.13
74 75 1.089481 ATGTAATGTGCAGCGTCCGG 61.089 55.000 0.00 0.00 0.00 5.14
75 76 0.026674 CATGTAATGTGCAGCGTCCG 59.973 55.000 0.00 0.00 40.20 4.79
76 77 3.903876 CATGTAATGTGCAGCGTCC 57.096 52.632 0.00 0.00 40.20 4.79
87 88 1.953559 CTAGGCGCCACACATGTAAT 58.046 50.000 31.54 5.89 0.00 1.89
88 89 0.742990 GCTAGGCGCCACACATGTAA 60.743 55.000 31.54 0.72 0.00 2.41
89 90 1.153449 GCTAGGCGCCACACATGTA 60.153 57.895 31.54 9.35 0.00 2.29
90 91 2.436646 GCTAGGCGCCACACATGT 60.437 61.111 31.54 8.51 0.00 3.21
91 92 2.124983 AGCTAGGCGCCACACATG 60.125 61.111 31.54 12.28 40.39 3.21
92 93 2.187946 GAGCTAGGCGCCACACAT 59.812 61.111 31.54 10.27 40.39 3.21
93 94 4.435436 CGAGCTAGGCGCCACACA 62.435 66.667 31.54 9.67 40.39 3.72
96 97 4.577246 CTCCGAGCTAGGCGCCAC 62.577 72.222 31.54 17.93 40.39 5.01
102 103 4.277593 CAGCGCCTCCGAGCTAGG 62.278 72.222 6.52 6.52 44.07 3.02
103 104 4.940593 GCAGCGCCTCCGAGCTAG 62.941 72.222 2.29 0.00 44.07 3.42
143 144 3.825160 TTCAGTCCACCGTGGCAGC 62.825 63.158 13.19 5.68 37.47 5.25
144 145 1.669115 CTTCAGTCCACCGTGGCAG 60.669 63.158 13.19 5.49 37.47 4.85
145 146 2.425592 CTTCAGTCCACCGTGGCA 59.574 61.111 13.19 0.00 37.47 4.92
146 147 1.961277 CACTTCAGTCCACCGTGGC 60.961 63.158 13.19 8.17 37.47 5.01
147 148 1.961277 GCACTTCAGTCCACCGTGG 60.961 63.158 11.73 11.73 39.43 4.94
148 149 0.813610 TTGCACTTCAGTCCACCGTG 60.814 55.000 0.00 0.00 0.00 4.94
149 150 0.814010 GTTGCACTTCAGTCCACCGT 60.814 55.000 0.00 0.00 0.00 4.83
150 151 1.831389 CGTTGCACTTCAGTCCACCG 61.831 60.000 0.00 0.00 0.00 4.94
151 152 1.941812 CGTTGCACTTCAGTCCACC 59.058 57.895 0.00 0.00 0.00 4.61
152 153 1.279840 GCGTTGCACTTCAGTCCAC 59.720 57.895 0.00 0.00 0.00 4.02
153 154 1.891919 GGCGTTGCACTTCAGTCCA 60.892 57.895 0.00 0.00 0.00 4.02
154 155 2.617274 GGGCGTTGCACTTCAGTCC 61.617 63.158 0.00 0.00 0.00 3.85
155 156 2.617274 GGGGCGTTGCACTTCAGTC 61.617 63.158 0.00 0.00 29.71 3.51
156 157 2.594592 GGGGCGTTGCACTTCAGT 60.595 61.111 0.00 0.00 29.71 3.41
157 158 3.365265 GGGGGCGTTGCACTTCAG 61.365 66.667 0.00 0.00 29.71 3.02
165 166 4.530857 CCTAGCTCGGGGGCGTTG 62.531 72.222 0.00 0.00 37.29 4.10
178 179 2.278857 CTACGGTGCAGCGCCTAG 60.279 66.667 35.78 25.87 0.00 3.02
179 180 3.833645 CCTACGGTGCAGCGCCTA 61.834 66.667 35.78 21.25 0.00 3.93
213 214 4.940593 TTTTTGTGCAGCGCCCGC 62.941 61.111 12.24 12.24 42.33 6.13
214 215 2.730604 CTTTTTGTGCAGCGCCCG 60.731 61.111 2.29 0.00 0.00 6.13
215 216 2.356194 CCTTTTTGTGCAGCGCCC 60.356 61.111 2.29 0.00 0.00 6.13
216 217 1.661509 GACCTTTTTGTGCAGCGCC 60.662 57.895 2.29 0.00 0.00 6.53
217 218 0.936297 CTGACCTTTTTGTGCAGCGC 60.936 55.000 0.00 0.00 0.00 5.92
218 219 0.318107 CCTGACCTTTTTGTGCAGCG 60.318 55.000 0.00 0.00 0.00 5.18
219 220 0.032540 CCCTGACCTTTTTGTGCAGC 59.967 55.000 0.00 0.00 0.00 5.25
220 221 0.675633 CCCCTGACCTTTTTGTGCAG 59.324 55.000 0.00 0.00 0.00 4.41
221 222 0.032615 ACCCCTGACCTTTTTGTGCA 60.033 50.000 0.00 0.00 0.00 4.57
222 223 0.389025 CACCCCTGACCTTTTTGTGC 59.611 55.000 0.00 0.00 0.00 4.57
223 224 1.408702 CACACCCCTGACCTTTTTGTG 59.591 52.381 0.00 0.00 0.00 3.33
224 225 1.286553 TCACACCCCTGACCTTTTTGT 59.713 47.619 0.00 0.00 0.00 2.83
225 226 2.065899 TCACACCCCTGACCTTTTTG 57.934 50.000 0.00 0.00 0.00 2.44
226 227 2.838637 TTCACACCCCTGACCTTTTT 57.161 45.000 0.00 0.00 0.00 1.94
227 228 2.838637 TTTCACACCCCTGACCTTTT 57.161 45.000 0.00 0.00 0.00 2.27
228 229 3.397955 ACTATTTCACACCCCTGACCTTT 59.602 43.478 0.00 0.00 0.00 3.11
229 230 2.986728 ACTATTTCACACCCCTGACCTT 59.013 45.455 0.00 0.00 0.00 3.50
230 231 2.632537 ACTATTTCACACCCCTGACCT 58.367 47.619 0.00 0.00 0.00 3.85
231 232 3.434940 AACTATTTCACACCCCTGACC 57.565 47.619 0.00 0.00 0.00 4.02
232 233 5.106830 CGTAAAACTATTTCACACCCCTGAC 60.107 44.000 0.00 0.00 0.00 3.51
233 234 4.998672 CGTAAAACTATTTCACACCCCTGA 59.001 41.667 0.00 0.00 0.00 3.86
234 235 4.155280 CCGTAAAACTATTTCACACCCCTG 59.845 45.833 0.00 0.00 0.00 4.45
235 236 4.329392 CCGTAAAACTATTTCACACCCCT 58.671 43.478 0.00 0.00 0.00 4.79
236 237 3.441222 CCCGTAAAACTATTTCACACCCC 59.559 47.826 0.00 0.00 0.00 4.95
237 238 3.119743 GCCCGTAAAACTATTTCACACCC 60.120 47.826 0.00 0.00 0.00 4.61
238 239 3.502979 TGCCCGTAAAACTATTTCACACC 59.497 43.478 0.00 0.00 0.00 4.16
239 240 4.214758 ACTGCCCGTAAAACTATTTCACAC 59.785 41.667 0.00 0.00 0.00 3.82
240 241 4.391155 ACTGCCCGTAAAACTATTTCACA 58.609 39.130 0.00 0.00 0.00 3.58
241 242 5.049267 TGAACTGCCCGTAAAACTATTTCAC 60.049 40.000 0.00 0.00 0.00 3.18
242 243 5.064558 TGAACTGCCCGTAAAACTATTTCA 58.935 37.500 0.00 0.00 0.00 2.69
243 244 5.616488 TGAACTGCCCGTAAAACTATTTC 57.384 39.130 0.00 0.00 0.00 2.17
244 245 6.349860 GGAATGAACTGCCCGTAAAACTATTT 60.350 38.462 0.00 0.00 0.00 1.40
245 246 5.124936 GGAATGAACTGCCCGTAAAACTATT 59.875 40.000 0.00 0.00 0.00 1.73
246 247 4.638865 GGAATGAACTGCCCGTAAAACTAT 59.361 41.667 0.00 0.00 0.00 2.12
247 248 4.004982 GGAATGAACTGCCCGTAAAACTA 58.995 43.478 0.00 0.00 0.00 2.24
248 249 2.817844 GGAATGAACTGCCCGTAAAACT 59.182 45.455 0.00 0.00 0.00 2.66
249 250 2.413634 CGGAATGAACTGCCCGTAAAAC 60.414 50.000 0.00 0.00 37.40 2.43
250 251 1.807742 CGGAATGAACTGCCCGTAAAA 59.192 47.619 0.00 0.00 37.40 1.52
251 252 1.444836 CGGAATGAACTGCCCGTAAA 58.555 50.000 0.00 0.00 37.40 2.01
252 253 3.146783 CGGAATGAACTGCCCGTAA 57.853 52.632 0.00 0.00 37.40 3.18
253 254 4.924019 CGGAATGAACTGCCCGTA 57.076 55.556 0.00 0.00 37.40 4.02
255 256 0.953471 TTCACGGAATGAACTGCCCG 60.953 55.000 0.00 0.00 42.62 6.13
256 257 2.941210 TTCACGGAATGAACTGCCC 58.059 52.632 0.00 0.00 42.62 5.36
263 264 4.094294 GGACGAAATCAATTCACGGAATGA 59.906 41.667 0.00 2.27 37.96 2.57
264 265 4.342772 GGACGAAATCAATTCACGGAATG 58.657 43.478 0.00 0.00 37.96 2.67
265 266 3.377172 GGGACGAAATCAATTCACGGAAT 59.623 43.478 0.00 0.00 37.96 3.01
266 267 2.745281 GGGACGAAATCAATTCACGGAA 59.255 45.455 0.00 0.00 37.96 4.30
267 268 2.289756 TGGGACGAAATCAATTCACGGA 60.290 45.455 0.00 0.00 37.96 4.69
268 269 2.080693 TGGGACGAAATCAATTCACGG 58.919 47.619 0.00 0.00 37.96 4.94
269 270 3.426159 CCTTGGGACGAAATCAATTCACG 60.426 47.826 0.00 0.00 37.96 4.35
270 271 3.506067 ACCTTGGGACGAAATCAATTCAC 59.494 43.478 0.00 0.00 37.96 3.18
271 272 3.756434 GACCTTGGGACGAAATCAATTCA 59.244 43.478 0.00 0.00 37.96 2.57
272 273 3.756434 TGACCTTGGGACGAAATCAATTC 59.244 43.478 0.00 0.00 34.52 2.17
273 274 3.761897 TGACCTTGGGACGAAATCAATT 58.238 40.909 0.00 0.00 0.00 2.32
274 275 3.433306 TGACCTTGGGACGAAATCAAT 57.567 42.857 0.00 0.00 0.00 2.57
275 276 2.940994 TGACCTTGGGACGAAATCAA 57.059 45.000 0.00 0.00 0.00 2.57
276 277 2.940994 TTGACCTTGGGACGAAATCA 57.059 45.000 0.00 0.00 0.00 2.57
277 278 4.783764 ATTTTGACCTTGGGACGAAATC 57.216 40.909 7.91 0.00 37.02 2.17
278 279 4.343814 ACAATTTTGACCTTGGGACGAAAT 59.656 37.500 7.91 7.91 40.96 2.17
279 280 3.702045 ACAATTTTGACCTTGGGACGAAA 59.298 39.130 0.00 4.51 35.83 3.46
280 281 3.292460 ACAATTTTGACCTTGGGACGAA 58.708 40.909 0.00 0.00 0.00 3.85
281 282 2.882137 GACAATTTTGACCTTGGGACGA 59.118 45.455 0.00 0.00 0.00 4.20
282 283 2.621055 TGACAATTTTGACCTTGGGACG 59.379 45.455 0.00 0.00 0.00 4.79
283 284 4.664150 TTGACAATTTTGACCTTGGGAC 57.336 40.909 0.00 0.00 0.00 4.46
284 285 5.885449 ATTTGACAATTTTGACCTTGGGA 57.115 34.783 0.00 0.00 0.00 4.37
285 286 6.727215 CAAATTTGACAATTTTGACCTTGGG 58.273 36.000 22.40 2.00 40.09 4.12
286 287 6.200808 GCAAATTTGACAATTTTGACCTTGG 58.799 36.000 27.56 9.61 40.09 3.61
287 288 6.200808 GGCAAATTTGACAATTTTGACCTTG 58.799 36.000 27.56 10.74 40.09 3.61
288 289 5.299028 GGGCAAATTTGACAATTTTGACCTT 59.701 36.000 33.72 5.33 40.09 3.50
289 290 4.821260 GGGCAAATTTGACAATTTTGACCT 59.179 37.500 33.72 5.89 40.09 3.85
290 291 4.023279 GGGGCAAATTTGACAATTTTGACC 60.023 41.667 33.51 33.51 40.09 4.02
291 292 4.023279 GGGGGCAAATTTGACAATTTTGAC 60.023 41.667 27.56 25.82 40.09 3.18
292 293 4.140536 GGGGGCAAATTTGACAATTTTGA 58.859 39.130 27.56 0.07 40.09 2.69
293 294 3.887716 TGGGGGCAAATTTGACAATTTTG 59.112 39.130 25.05 22.48 40.09 2.44
294 295 3.888323 GTGGGGGCAAATTTGACAATTTT 59.112 39.130 25.05 2.88 40.09 1.82
295 296 3.485394 GTGGGGGCAAATTTGACAATTT 58.515 40.909 25.05 0.00 42.37 1.82
296 297 2.549778 CGTGGGGGCAAATTTGACAATT 60.550 45.455 25.05 0.00 38.18 2.32
297 298 1.001860 CGTGGGGGCAAATTTGACAAT 59.998 47.619 25.05 0.00 38.18 2.71
298 299 0.390860 CGTGGGGGCAAATTTGACAA 59.609 50.000 25.05 7.72 38.18 3.18
299 300 2.045280 CGTGGGGGCAAATTTGACA 58.955 52.632 25.05 12.60 38.18 3.58
300 301 1.374125 GCGTGGGGGCAAATTTGAC 60.374 57.895 22.31 19.34 34.70 3.18
301 302 2.925262 CGCGTGGGGGCAAATTTGA 61.925 57.895 22.31 0.00 0.00 2.69
302 303 2.432285 CGCGTGGGGGCAAATTTG 60.432 61.111 14.03 14.03 0.00 2.32
345 346 6.300902 CGAAATGCTAAACTGAAAACGAGAAG 59.699 38.462 0.00 0.00 0.00 2.85
457 458 0.531974 TGTGTTCTCCCTGCAACGAC 60.532 55.000 0.00 0.00 0.00 4.34
458 459 0.396435 ATGTGTTCTCCCTGCAACGA 59.604 50.000 0.00 0.00 0.00 3.85
459 460 1.732259 GTATGTGTTCTCCCTGCAACG 59.268 52.381 0.00 0.00 0.00 4.10
541 546 1.869754 CGGAGCCGATTCATGTACCAG 60.870 57.143 2.00 0.00 42.83 4.00
569 574 2.025793 TGTTGTTTCTGTCTCCACCCAA 60.026 45.455 0.00 0.00 0.00 4.12
696 701 6.046593 TCCTAATTAATCTACTGGTGTTGCG 58.953 40.000 0.00 0.00 0.00 4.85
699 704 7.934120 GCTCATCCTAATTAATCTACTGGTGTT 59.066 37.037 0.00 0.00 0.00 3.32
730 735 7.953005 TCAGCTTCTATGATTCTATCCCTAG 57.047 40.000 0.00 0.00 0.00 3.02
731 736 8.907829 ATTCAGCTTCTATGATTCTATCCCTA 57.092 34.615 0.00 0.00 0.00 3.53
739 746 9.591404 CGTTAAATGATTCAGCTTCTATGATTC 57.409 33.333 0.00 0.00 0.00 2.52
740 747 8.072567 GCGTTAAATGATTCAGCTTCTATGATT 58.927 33.333 0.00 0.00 0.00 2.57
741 748 7.308229 GGCGTTAAATGATTCAGCTTCTATGAT 60.308 37.037 0.00 0.00 0.00 2.45
742 749 6.017934 GGCGTTAAATGATTCAGCTTCTATGA 60.018 38.462 0.00 0.00 0.00 2.15
743 750 6.138761 GGCGTTAAATGATTCAGCTTCTATG 58.861 40.000 0.00 0.00 0.00 2.23
780 787 1.716503 AGGGTATTGGAGGGCAAAACT 59.283 47.619 0.00 0.00 0.00 2.66
817 1290 9.211485 CCATGCAGTTAAATCTTTTTGAGAAAT 57.789 29.630 0.00 0.00 38.06 2.17
1063 1537 3.480470 GCTATAGAGCTGGAATTTGCCA 58.520 45.455 3.21 0.00 45.98 4.92
1183 1657 2.282745 AAGTTCCCAGGCAGCTGC 60.283 61.111 30.88 30.88 41.14 5.25
1380 1855 6.595772 GTTCCTGAACAATAGAGCATACAG 57.404 41.667 5.18 0.00 40.84 2.74
1752 2278 2.127708 GCATTAGGAGGGGAGGAAGAA 58.872 52.381 0.00 0.00 0.00 2.52
1758 2284 0.980423 GGCTAGCATTAGGAGGGGAG 59.020 60.000 18.24 0.00 0.00 4.30
2543 3075 2.490903 AGCTCAAGTGCAATCCAATGTC 59.509 45.455 0.00 0.00 34.99 3.06
2682 3220 9.535878 GCTTCAATATAAGATATAGTAGCCACC 57.464 37.037 0.00 0.00 0.00 4.61
2905 3444 2.979814 TCACTACATGCGCATTACCT 57.020 45.000 22.81 6.00 0.00 3.08
2926 3465 6.481954 ACACGAATTAATCACAGAAAGGAC 57.518 37.500 0.00 0.00 0.00 3.85
2976 3515 2.163010 CACTTGGCCTTGAGCATAACTG 59.837 50.000 3.32 0.00 46.50 3.16
2977 3516 2.224867 ACACTTGGCCTTGAGCATAACT 60.225 45.455 3.32 0.00 46.50 2.24
2978 3517 2.162681 ACACTTGGCCTTGAGCATAAC 58.837 47.619 3.32 0.00 46.50 1.89
3033 3572 5.833131 AGAGTTAGCAGGGAAATGTGAAAAA 59.167 36.000 0.00 0.00 0.00 1.94
3084 3623 1.664874 GGACGTTGGCAATTTCCGTTC 60.665 52.381 13.67 8.96 0.00 3.95
3568 4217 0.316204 GGCACAAGCAGCAATGTTCT 59.684 50.000 0.00 0.00 44.61 3.01
3771 4423 6.667558 AGAAGTAGGAATACCCCTTTATCG 57.332 41.667 0.00 0.00 37.74 2.92
3782 4434 7.626084 TCCAGGAAATTGGTAGAAGTAGGAATA 59.374 37.037 0.00 0.00 39.35 1.75
3796 4448 6.523840 TCTCAATTGTTTTCCAGGAAATTGG 58.476 36.000 15.75 10.47 38.29 3.16
3812 4464 2.172293 CTCCCTTCCCCTCTCTCAATTG 59.828 54.545 0.00 0.00 0.00 2.32
3826 4490 1.688197 CTGCAGGATCTCTCTCCCTTC 59.312 57.143 5.57 0.00 35.79 3.46
3827 4491 1.008206 ACTGCAGGATCTCTCTCCCTT 59.992 52.381 19.93 0.00 35.79 3.95
3849 4513 3.074412 CCTAATAACTAATGGGCTGCCG 58.926 50.000 13.40 0.22 0.00 5.69
4005 4673 5.962423 GCAAACAAAATTTTACATTGCGTGT 59.038 32.000 21.47 6.26 44.95 4.49
4008 8430 5.505286 TGGCAAACAAAATTTTACATTGCG 58.495 33.333 25.20 9.63 41.80 4.85
4031 8453 7.872483 ACATGGTGCGAATTCTTCTAAAAATTT 59.128 29.630 3.52 0.00 0.00 1.82
4146 8615 7.972832 ATATTTTTAAACGCCGGATCATCTA 57.027 32.000 5.05 0.00 0.00 1.98
4174 8643 8.863049 CATGAACCTTTTAAGTAAATGTCATGC 58.137 33.333 12.36 0.00 31.74 4.06
4628 9306 0.958822 GTGTGGGCCAAAACTACCAG 59.041 55.000 8.40 0.00 32.84 4.00
4649 9329 1.737236 TCTCGCCATGCAACATGTTAC 59.263 47.619 11.53 6.28 0.00 2.50
4650 9330 2.009051 CTCTCGCCATGCAACATGTTA 58.991 47.619 11.53 0.00 0.00 2.41
4653 9333 1.596260 CTACTCTCGCCATGCAACATG 59.404 52.381 0.00 0.48 0.00 3.21
4657 9337 1.519234 CGCTACTCTCGCCATGCAA 60.519 57.895 0.00 0.00 0.00 4.08
4669 9349 1.407258 GAGCCTCATTCACTCGCTACT 59.593 52.381 0.00 0.00 0.00 2.57
4690 9370 0.819259 CCACAAGGTCCACAGTGGTG 60.819 60.000 19.65 12.49 44.95 4.17
4714 9394 8.792831 TTGTTAGTACACGAAGAAACTAGAAG 57.207 34.615 0.00 0.00 32.98 2.85
4769 9450 1.328680 CTTCTAGTACTTCGCGCGGTA 59.671 52.381 31.69 21.76 0.00 4.02
4997 9683 2.132762 GTTCCCGCGGAATACACTATG 58.867 52.381 30.73 5.39 44.04 2.23
4999 9685 1.184431 TGTTCCCGCGGAATACACTA 58.816 50.000 30.73 2.72 44.04 2.74
5011 9697 8.706492 TTTTATGTACTACACTTATGTTCCCG 57.294 34.615 0.00 0.00 40.48 5.14
5025 9711 6.425721 ACTTTGTGCTTCGCTTTTATGTACTA 59.574 34.615 0.00 0.00 0.00 1.82
5064 9750 1.529865 GTACTGTCAGGCACGAAAACC 59.470 52.381 4.53 0.00 0.00 3.27
5076 9762 0.034767 ATCCCTCGACGGTACTGTCA 60.035 55.000 29.50 17.62 38.84 3.58
5105 9791 0.685785 TGTGTGCTTGCCCTCCAAAA 60.686 50.000 0.00 0.00 31.94 2.44
5127 9814 4.943705 TCTCTTTTTCGCCTCAGCATAATT 59.056 37.500 0.00 0.00 39.83 1.40
5132 9819 1.609061 CCTCTCTTTTTCGCCTCAGCA 60.609 52.381 0.00 0.00 39.83 4.41
5133 9820 1.082690 CCTCTCTTTTTCGCCTCAGC 58.917 55.000 0.00 0.00 0.00 4.26
5134 9821 2.751166 TCCTCTCTTTTTCGCCTCAG 57.249 50.000 0.00 0.00 0.00 3.35
5167 9858 0.980231 CTCCACCTGCTAGAAGGCCT 60.980 60.000 17.69 0.00 41.46 5.19
5176 9867 0.910088 GGGTCTTACCTCCACCTGCT 60.910 60.000 0.00 0.00 38.64 4.24
5177 9868 0.910088 AGGGTCTTACCTCCACCTGC 60.910 60.000 0.00 0.00 38.64 4.85
5178 9869 3.401032 AGGGTCTTACCTCCACCTG 57.599 57.895 0.00 0.00 38.64 4.00
5197 9888 0.249238 GACGCACTAGAGGCTGGATG 60.249 60.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.