Multiple sequence alignment - TraesCS2A01G266000

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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 TraesCS2A01G266000 chr2A 100.000 3118 0 0 1 3118 422786011 422782894 0.000000e+00 5758
1 TraesCS2A01G266000 chr2A 97.397 461 11 1 2659 3118 422921241 422921701 0.000000e+00 784
2 TraesCS2A01G266000 chr2A 85.118 551 76 4 1177 1727 423176419 423176963 2.720000e-155 558
3 TraesCS2A01G266000 chr2A 94.672 244 12 1 1 244 422791237 422790995 8.160000e-101 377
4 TraesCS2A01G266000 chr2B 90.057 2122 107 46 138 2209 381521367 381519300 0.000000e+00 2654
5 TraesCS2A01G266000 chr2B 83.077 585 85 11 1145 1728 381317147 381316576 1.280000e-143 520
6 TraesCS2A01G266000 chr2B 84.116 277 18 2 2465 2715 381518870 381518594 8.640000e-61 244
7 TraesCS2A01G266000 chr2B 91.667 144 9 3 2302 2444 381519183 381519042 2.450000e-46 196
8 TraesCS2A01G266000 chr2B 82.500 160 22 4 2958 3112 381504287 381504129 5.420000e-28 135
9 TraesCS2A01G266000 chr2D 92.291 1816 78 21 799 2603 313811938 313810174 0.000000e+00 2521
10 TraesCS2A01G266000 chr2D 89.820 501 29 8 315 814 313814578 313814099 9.500000e-175 623
11 TraesCS2A01G266000 chr2D 85.420 583 73 9 1145 1727 313714789 313714219 2.070000e-166 595
12 TraesCS2A01G266000 chr2D 86.458 384 43 5 2740 3118 313809043 313808664 2.240000e-111 412
13 TraesCS2A01G266000 chr2D 94.783 115 6 0 2601 2715 313810146 313810032 2.470000e-41 180
14 TraesCS2A01G266000 chr5A 87.379 103 13 0 1322 1424 596044627 596044729 5.460000e-23 119
15 TraesCS2A01G266000 chr5B 85.321 109 16 0 1322 1430 584292166 584292274 2.540000e-21 113


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 TraesCS2A01G266000 chr2A 422782894 422786011 3117 True 5758.000000 5758 100.000000 1 3118 1 chr2A.!!$R1 3117
1 TraesCS2A01G266000 chr2A 423176419 423176963 544 False 558.000000 558 85.118000 1177 1727 1 chr2A.!!$F2 550
2 TraesCS2A01G266000 chr2B 381518594 381521367 2773 True 1031.333333 2654 88.613333 138 2715 3 chr2B.!!$R3 2577
3 TraesCS2A01G266000 chr2B 381316576 381317147 571 True 520.000000 520 83.077000 1145 1728 1 chr2B.!!$R1 583
4 TraesCS2A01G266000 chr2D 313808664 313814578 5914 True 934.000000 2521 90.838000 315 3118 4 chr2D.!!$R2 2803
5 TraesCS2A01G266000 chr2D 313714219 313714789 570 True 595.000000 595 85.420000 1145 1727 1 chr2D.!!$R1 582

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
120 121 0.031721 GGGACTGGGTATTAGCGTCG 59.968 60.0 0.00 0.00 0.00 5.12 F
1828 4069 0.035056 ATTCTGGAACCAGCGGGAAG 60.035 55.0 10.86 1.66 43.31 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 4079 0.734889 GCGACATCAATTCCCACCTG 59.265 55.0 0.00 0.00 0.00 4.00 R
2955 6436 0.332293 TGGAGATGCAATGCTTCCCA 59.668 50.0 19.51 19.51 33.95 4.37 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
31 32 9.727627 TTGATGAAAATTGCACCAAAAATAAAC 57.272 25.926 0.00 0.00 0.00 2.01
32 33 8.896744 TGATGAAAATTGCACCAAAAATAAACA 58.103 25.926 0.00 0.00 0.00 2.83
33 34 9.727627 GATGAAAATTGCACCAAAAATAAACAA 57.272 25.926 0.00 0.00 0.00 2.83
34 35 8.902040 TGAAAATTGCACCAAAAATAAACAAC 57.098 26.923 0.00 0.00 0.00 3.32
35 36 8.734386 TGAAAATTGCACCAAAAATAAACAACT 58.266 25.926 0.00 0.00 0.00 3.16
36 37 8.908172 AAAATTGCACCAAAAATAAACAACTG 57.092 26.923 0.00 0.00 0.00 3.16
37 38 5.476752 TTGCACCAAAAATAAACAACTGC 57.523 34.783 0.00 0.00 0.00 4.40
38 39 3.873952 TGCACCAAAAATAAACAACTGCC 59.126 39.130 0.00 0.00 0.00 4.85
39 40 3.873952 GCACCAAAAATAAACAACTGCCA 59.126 39.130 0.00 0.00 0.00 4.92
40 41 4.514816 GCACCAAAAATAAACAACTGCCAT 59.485 37.500 0.00 0.00 0.00 4.40
41 42 5.560567 GCACCAAAAATAAACAACTGCCATG 60.561 40.000 0.00 0.00 0.00 3.66
42 43 5.526846 CACCAAAAATAAACAACTGCCATGT 59.473 36.000 0.00 0.00 0.00 3.21
43 44 6.038050 CACCAAAAATAAACAACTGCCATGTT 59.962 34.615 0.00 0.00 42.56 2.71
45 46 7.121907 ACCAAAAATAAACAACTGCCATGTTTT 59.878 29.630 14.28 3.74 45.97 2.43
46 47 7.972832 CCAAAAATAAACAACTGCCATGTTTTT 59.027 29.630 14.28 6.58 45.97 1.94
70 71 2.046023 CCATCTGGCAGGTTCGCA 60.046 61.111 15.73 0.00 0.00 5.10
71 72 2.110967 CCATCTGGCAGGTTCGCAG 61.111 63.158 15.73 0.00 0.00 5.18
72 73 1.078918 CATCTGGCAGGTTCGCAGA 60.079 57.895 15.73 0.00 0.00 4.26
73 74 1.088340 CATCTGGCAGGTTCGCAGAG 61.088 60.000 15.73 0.00 38.43 3.35
74 75 2.249413 ATCTGGCAGGTTCGCAGAGG 62.249 60.000 15.73 0.00 38.43 3.69
75 76 3.241530 TGGCAGGTTCGCAGAGGT 61.242 61.111 0.00 0.00 38.43 3.85
76 77 2.435059 GGCAGGTTCGCAGAGGTC 60.435 66.667 0.00 0.00 38.43 3.85
77 78 2.343758 GCAGGTTCGCAGAGGTCA 59.656 61.111 0.00 0.00 38.43 4.02
78 79 1.078848 GCAGGTTCGCAGAGGTCAT 60.079 57.895 0.00 0.00 38.43 3.06
79 80 1.364626 GCAGGTTCGCAGAGGTCATG 61.365 60.000 0.00 0.00 38.43 3.07
80 81 1.078848 AGGTTCGCAGAGGTCATGC 60.079 57.895 0.00 0.00 38.43 4.06
85 86 3.479370 GCAGAGGTCATGCGTGTC 58.521 61.111 5.68 0.00 33.31 3.67
86 87 1.374631 GCAGAGGTCATGCGTGTCA 60.375 57.895 5.68 0.00 33.31 3.58
87 88 1.357258 GCAGAGGTCATGCGTGTCAG 61.357 60.000 5.68 0.00 33.31 3.51
88 89 1.079543 AGAGGTCATGCGTGTCAGC 60.080 57.895 5.68 0.00 37.71 4.26
89 90 1.079543 GAGGTCATGCGTGTCAGCT 60.080 57.895 5.68 2.21 38.13 4.24
90 91 0.173481 GAGGTCATGCGTGTCAGCTA 59.827 55.000 5.68 0.00 38.13 3.32
91 92 0.608130 AGGTCATGCGTGTCAGCTAA 59.392 50.000 5.68 0.00 38.13 3.09
92 93 0.721718 GGTCATGCGTGTCAGCTAAC 59.278 55.000 5.68 0.00 38.13 2.34
93 94 0.366871 GTCATGCGTGTCAGCTAACG 59.633 55.000 5.68 10.49 42.61 3.18
94 95 0.038618 TCATGCGTGTCAGCTAACGT 60.039 50.000 14.79 0.00 41.76 3.99
95 96 0.790207 CATGCGTGTCAGCTAACGTT 59.210 50.000 5.88 5.88 41.76 3.99
96 97 1.068474 ATGCGTGTCAGCTAACGTTC 58.932 50.000 2.82 0.00 41.76 3.95
97 98 0.249114 TGCGTGTCAGCTAACGTTCA 60.249 50.000 2.82 0.00 41.76 3.18
98 99 0.161024 GCGTGTCAGCTAACGTTCAC 59.839 55.000 2.82 4.67 41.76 3.18
99 100 1.767289 CGTGTCAGCTAACGTTCACT 58.233 50.000 2.82 0.00 35.13 3.41
100 101 1.452025 CGTGTCAGCTAACGTTCACTG 59.548 52.381 19.35 19.35 35.13 3.66
101 102 1.792949 GTGTCAGCTAACGTTCACTGG 59.207 52.381 22.95 10.33 0.00 4.00
102 103 1.270094 TGTCAGCTAACGTTCACTGGG 60.270 52.381 22.95 6.20 0.00 4.45
103 104 0.320374 TCAGCTAACGTTCACTGGGG 59.680 55.000 22.95 5.63 0.00 4.96
104 105 0.320374 CAGCTAACGTTCACTGGGGA 59.680 55.000 18.20 0.00 0.00 4.81
105 106 0.320697 AGCTAACGTTCACTGGGGAC 59.679 55.000 2.82 0.00 0.00 4.46
106 107 0.320697 GCTAACGTTCACTGGGGACT 59.679 55.000 2.82 0.00 0.00 3.85
107 108 1.939838 GCTAACGTTCACTGGGGACTG 60.940 57.143 2.82 0.00 0.00 3.51
108 109 0.682852 TAACGTTCACTGGGGACTGG 59.317 55.000 2.82 0.00 0.00 4.00
109 110 2.052047 AACGTTCACTGGGGACTGGG 62.052 60.000 0.00 0.00 0.00 4.45
110 111 2.516888 CGTTCACTGGGGACTGGGT 61.517 63.158 0.00 0.00 33.79 4.51
111 112 1.189524 CGTTCACTGGGGACTGGGTA 61.190 60.000 0.00 0.00 33.79 3.69
112 113 1.286248 GTTCACTGGGGACTGGGTAT 58.714 55.000 0.00 0.00 33.79 2.73
113 114 1.633945 GTTCACTGGGGACTGGGTATT 59.366 52.381 0.00 0.00 33.79 1.89
114 115 2.841881 GTTCACTGGGGACTGGGTATTA 59.158 50.000 0.00 0.00 33.79 0.98
115 116 2.759355 TCACTGGGGACTGGGTATTAG 58.241 52.381 0.00 0.00 33.79 1.73
116 117 1.141053 CACTGGGGACTGGGTATTAGC 59.859 57.143 0.00 0.00 0.00 3.09
117 118 0.393077 CTGGGGACTGGGTATTAGCG 59.607 60.000 0.00 0.00 0.00 4.26
118 119 0.325860 TGGGGACTGGGTATTAGCGT 60.326 55.000 0.00 0.00 0.00 5.07
119 120 0.391966 GGGGACTGGGTATTAGCGTC 59.608 60.000 0.00 0.00 0.00 5.19
120 121 0.031721 GGGACTGGGTATTAGCGTCG 59.968 60.000 0.00 0.00 0.00 5.12
121 122 0.743097 GGACTGGGTATTAGCGTCGT 59.257 55.000 0.00 0.00 0.00 4.34
122 123 1.135721 GGACTGGGTATTAGCGTCGTT 59.864 52.381 0.00 0.00 0.00 3.85
123 124 2.358898 GGACTGGGTATTAGCGTCGTTA 59.641 50.000 0.00 0.00 0.00 3.18
124 125 3.181487 GGACTGGGTATTAGCGTCGTTAA 60.181 47.826 3.94 3.94 0.00 2.01
125 126 4.500375 GGACTGGGTATTAGCGTCGTTAAT 60.500 45.833 16.91 16.91 0.00 1.40
126 127 5.014808 ACTGGGTATTAGCGTCGTTAATT 57.985 39.130 17.75 4.82 0.00 1.40
127 128 6.147864 ACTGGGTATTAGCGTCGTTAATTA 57.852 37.500 17.75 4.00 0.00 1.40
128 129 6.211515 ACTGGGTATTAGCGTCGTTAATTAG 58.788 40.000 17.75 13.38 0.00 1.73
129 130 6.039717 ACTGGGTATTAGCGTCGTTAATTAGA 59.960 38.462 17.75 0.00 0.00 2.10
130 131 6.441274 TGGGTATTAGCGTCGTTAATTAGAG 58.559 40.000 17.75 0.00 0.00 2.43
131 132 5.860716 GGGTATTAGCGTCGTTAATTAGAGG 59.139 44.000 17.75 0.00 0.00 3.69
132 133 5.860716 GGTATTAGCGTCGTTAATTAGAGGG 59.139 44.000 17.75 0.00 0.00 4.30
133 134 4.989279 TTAGCGTCGTTAATTAGAGGGT 57.011 40.909 0.00 5.01 36.95 4.34
134 135 3.881937 AGCGTCGTTAATTAGAGGGTT 57.118 42.857 0.00 0.00 30.24 4.11
135 136 3.778618 AGCGTCGTTAATTAGAGGGTTC 58.221 45.455 0.00 0.00 30.24 3.62
136 137 2.533129 GCGTCGTTAATTAGAGGGTTCG 59.467 50.000 0.00 0.00 0.00 3.95
160 161 9.168451 TCGATGTAGTCTTTATGGCAAAATAAA 57.832 29.630 0.00 0.00 32.47 1.40
213 215 2.417719 ACTCTTACAAGGACCAGGGT 57.582 50.000 0.00 0.00 0.00 4.34
227 229 4.022589 GGACCAGGGTAAAAACAAGTAAGC 60.023 45.833 0.00 0.00 0.00 3.09
254 256 2.225491 TCGCTTATTGAACTTGGTGTGC 59.775 45.455 0.00 0.00 0.00 4.57
255 257 2.031245 CGCTTATTGAACTTGGTGTGCA 60.031 45.455 0.00 0.00 30.91 4.57
257 259 3.983344 GCTTATTGAACTTGGTGTGCAAG 59.017 43.478 0.00 0.00 46.49 4.01
258 260 4.549458 CTTATTGAACTTGGTGTGCAAGG 58.451 43.478 0.00 0.00 46.49 3.61
259 261 1.846007 TTGAACTTGGTGTGCAAGGT 58.154 45.000 0.00 0.00 39.19 3.50
260 262 1.102154 TGAACTTGGTGTGCAAGGTG 58.898 50.000 0.00 0.00 29.56 4.00
261 263 0.249031 GAACTTGGTGTGCAAGGTGC 60.249 55.000 0.00 0.00 45.29 5.01
316 319 2.106477 AGTTTGCCTAGCTGAGAAGC 57.894 50.000 0.00 0.00 0.00 3.86
319 322 2.105006 TTGCCTAGCTGAGAAGCAAG 57.895 50.000 0.00 0.00 38.45 4.01
325 342 1.236628 AGCTGAGAAGCAAGCTTGTG 58.763 50.000 26.55 4.51 36.26 3.33
331 348 2.099756 GAGAAGCAAGCTTGTGTGGTTT 59.900 45.455 26.55 11.96 35.69 3.27
360 377 6.543831 AGCTTATTTGCCGATTAAGATGTCTT 59.456 34.615 0.45 0.45 39.85 3.01
402 425 7.520119 TGTTTGTAGTATTCTGATTGTAGCG 57.480 36.000 0.00 0.00 0.00 4.26
422 445 2.518949 GGCATACGACAAATTGCTGTG 58.481 47.619 0.00 0.00 35.46 3.66
427 450 2.013400 ACGACAAATTGCTGTGACACA 58.987 42.857 8.26 8.26 0.00 3.72
439 462 6.832520 TGCTGTGACACATGGTTTTATAAT 57.167 33.333 9.11 0.00 0.00 1.28
440 463 7.929941 TGCTGTGACACATGGTTTTATAATA 57.070 32.000 9.11 0.00 0.00 0.98
441 464 8.341892 TGCTGTGACACATGGTTTTATAATAA 57.658 30.769 9.11 0.00 0.00 1.40
516 540 9.859427 ATAAATAATTGACAGTGTGATTTGGTG 57.141 29.630 0.00 0.00 0.00 4.17
547 571 2.431683 TGCTGCTCCAACAGGACC 59.568 61.111 0.00 0.00 38.16 4.46
565 589 1.263217 ACCGTGATTTCGTCTTTGTGC 59.737 47.619 0.00 0.00 0.00 4.57
601 625 8.322828 TGCTCAGGTTACCAATAATTTACAGTA 58.677 33.333 3.51 0.00 0.00 2.74
681 712 0.734942 CTACCGCGGTTTCACGACAT 60.735 55.000 38.94 9.80 35.47 3.06
682 713 0.525311 TACCGCGGTTTCACGACATA 59.475 50.000 38.94 11.67 35.47 2.29
683 714 1.010419 ACCGCGGTTTCACGACATAC 61.010 55.000 28.70 0.00 35.47 2.39
684 715 0.734942 CCGCGGTTTCACGACATACT 60.735 55.000 19.50 0.00 35.47 2.12
685 716 0.365523 CGCGGTTTCACGACATACTG 59.634 55.000 0.00 0.00 35.47 2.74
746 777 1.028130 GGGTCAGTACGTAGGTAGGC 58.972 60.000 0.00 0.00 0.00 3.93
748 779 1.373570 GTCAGTACGTAGGTAGGCGT 58.626 55.000 0.00 0.00 44.02 5.68
749 780 2.550978 GTCAGTACGTAGGTAGGCGTA 58.449 52.381 0.00 0.00 41.77 4.42
871 3078 2.375146 ACAAAATATCCCGAGCCCAAC 58.625 47.619 0.00 0.00 0.00 3.77
908 3115 4.389576 CAAACGCCAGCCTGTCGC 62.390 66.667 0.00 0.00 37.98 5.19
981 3193 2.166664 CTCCTCCTATATAACCAGCGCC 59.833 54.545 2.29 0.00 0.00 6.53
1030 3242 0.388659 ATCGCCATCTCAGTCTCAGC 59.611 55.000 0.00 0.00 0.00 4.26
1031 3243 0.967380 TCGCCATCTCAGTCTCAGCA 60.967 55.000 0.00 0.00 0.00 4.41
1032 3244 0.108472 CGCCATCTCAGTCTCAGCAA 60.108 55.000 0.00 0.00 0.00 3.91
1033 3245 1.472904 CGCCATCTCAGTCTCAGCAAT 60.473 52.381 0.00 0.00 0.00 3.56
1034 3246 2.223900 CGCCATCTCAGTCTCAGCAATA 60.224 50.000 0.00 0.00 0.00 1.90
1035 3247 3.391965 GCCATCTCAGTCTCAGCAATAG 58.608 50.000 0.00 0.00 0.00 1.73
1045 3257 3.044156 TCTCAGCAATAGCATTCCTCCT 58.956 45.455 0.00 0.00 45.49 3.69
1113 3346 4.363990 CACGACGGCACCAGCTCT 62.364 66.667 0.00 0.00 41.70 4.09
1114 3347 3.616721 ACGACGGCACCAGCTCTT 61.617 61.111 0.00 0.00 41.70 2.85
1471 3704 4.681978 GAGGACGTGGCCGCACTT 62.682 66.667 18.18 5.94 37.70 3.16
1642 3875 1.811679 GCTGGTAGTCAAGAGGCGC 60.812 63.158 0.00 0.00 0.00 6.53
1672 3905 2.890371 GTAAAGAGCGCCGGGAGA 59.110 61.111 2.29 0.00 0.00 3.71
1733 3974 1.024579 ATGCGAGTAAACCGGCCTTG 61.025 55.000 0.00 0.00 0.00 3.61
1828 4069 0.035056 ATTCTGGAACCAGCGGGAAG 60.035 55.000 10.86 1.66 43.31 3.46
1838 4079 2.821810 GCGGGAAGAGAGCAAGGC 60.822 66.667 0.00 0.00 0.00 4.35
2040 4281 9.424319 AGATTTAGCATGTGTATATTTCGTAGG 57.576 33.333 0.00 0.00 0.00 3.18
2042 4283 8.812147 TTTAGCATGTGTATATTTCGTAGGAG 57.188 34.615 0.00 0.00 0.00 3.69
2129 4371 9.694137 AAACAGTGAACATAAACTAGAGTACTC 57.306 33.333 15.41 15.41 0.00 2.59
2132 4374 9.130312 CAGTGAACATAAACTAGAGTACTCAAC 57.870 37.037 24.44 0.00 0.00 3.18
2219 4461 8.211198 ACGTTCGAAACTTGCAATTAAATTAG 57.789 30.769 0.00 0.00 0.00 1.73
2267 4595 8.863872 AGTAGTACTAAACATTTGCCATTTCT 57.136 30.769 3.61 0.00 0.00 2.52
2289 4617 7.373617 TCTATGATTAAGGGCTTCATGTACA 57.626 36.000 0.00 0.00 32.58 2.90
2346 4674 4.554363 CTGGGACTACTCCGCGCG 62.554 72.222 25.67 25.67 37.46 6.86
2440 4768 1.585214 CGTGTAGATTAAACCCGCGAC 59.415 52.381 8.23 0.00 0.00 5.19
2441 4769 1.585214 GTGTAGATTAAACCCGCGACG 59.415 52.381 8.23 0.00 0.00 5.12
2443 4771 0.528249 TAGATTAAACCCGCGACGGC 60.528 55.000 8.23 0.00 46.86 5.68
2444 4772 2.816360 GATTAAACCCGCGACGGCC 61.816 63.158 8.23 0.00 46.86 6.13
2478 4964 0.029834 ACTTACTGTGACGCGTCGTT 59.970 50.000 31.88 18.65 41.37 3.85
2486 4972 0.931702 TGACGCGTCGTTGAATTTGT 59.068 45.000 31.88 0.00 41.37 2.83
2490 4976 4.385146 TGACGCGTCGTTGAATTTGTAATA 59.615 37.500 31.88 7.70 41.37 0.98
2499 4985 7.382759 GTCGTTGAATTTGTAATAAGGGCAAAA 59.617 33.333 0.00 0.00 36.00 2.44
2500 4986 7.926555 TCGTTGAATTTGTAATAAGGGCAAAAA 59.073 29.630 0.00 0.00 36.00 1.94
2536 5022 1.119684 GGAGGGCAAAGTTTGTGGTT 58.880 50.000 16.70 1.22 0.00 3.67
2576 5063 1.304282 CCCCATGCTGTGCCTACTT 59.696 57.895 0.00 0.00 0.00 2.24
2683 5200 1.336609 GCCTACAAGTTCGGACGTTCT 60.337 52.381 0.00 0.00 0.00 3.01
2684 5201 2.865276 GCCTACAAGTTCGGACGTTCTT 60.865 50.000 0.00 0.00 0.00 2.52
2715 5232 4.938832 CGTTCTTTCCCCATACAACATGTA 59.061 41.667 0.00 0.00 37.24 2.29
2717 5234 6.764085 CGTTCTTTCCCCATACAACATGTATA 59.236 38.462 0.00 0.00 41.28 1.47
2719 5236 9.787435 GTTCTTTCCCCATACAACATGTATATA 57.213 33.333 0.00 0.00 41.28 0.86
2765 6246 7.875327 ATAGTGTTGTTCATACCAAATACCC 57.125 36.000 0.00 0.00 0.00 3.69
2773 6254 6.098409 TGTTCATACCAAATACCCTCTCTCTC 59.902 42.308 0.00 0.00 0.00 3.20
2817 6298 5.204833 CAAACATCAACAACAACGAGTAGG 58.795 41.667 0.00 0.00 0.00 3.18
2820 6301 4.750098 ACATCAACAACAACGAGTAGGAAG 59.250 41.667 0.00 0.00 0.00 3.46
2826 6307 5.425630 ACAACAACGAGTAGGAAGTTTTCT 58.574 37.500 0.00 0.00 0.00 2.52
2828 6309 5.019785 ACAACGAGTAGGAAGTTTTCTGT 57.980 39.130 0.00 0.00 0.00 3.41
2841 6322 7.173390 AGGAAGTTTTCTGTGAACTAAGCATAC 59.827 37.037 0.00 0.00 36.38 2.39
2853 6334 6.382859 TGAACTAAGCATACCTCAGATGGTTA 59.617 38.462 6.98 6.98 41.83 2.85
2865 6346 6.013379 ACCTCAGATGGTTAGATTCTTTGTGA 60.013 38.462 0.00 0.00 36.89 3.58
2895 6376 2.022718 CCATAGGGAGGAGAGGAAGG 57.977 60.000 0.00 0.00 35.59 3.46
2899 6380 1.215679 AGGGAGGAGAGGAAGGACGA 61.216 60.000 0.00 0.00 0.00 4.20
2900 6381 0.753848 GGGAGGAGAGGAAGGACGAG 60.754 65.000 0.00 0.00 0.00 4.18
2954 6435 3.818787 CCGCACCATGGCTGCTTC 61.819 66.667 26.29 8.28 32.03 3.86
2955 6436 2.749044 CGCACCATGGCTGCTTCT 60.749 61.111 26.29 0.94 32.03 2.85
2974 6455 0.332293 TGGGAAGCATTGCATCTCCA 59.668 50.000 19.81 17.69 38.65 3.86
2976 6457 2.037144 GGGAAGCATTGCATCTCCATT 58.963 47.619 19.81 2.58 38.65 3.16
2977 6458 2.433239 GGGAAGCATTGCATCTCCATTT 59.567 45.455 19.81 1.95 38.65 2.32
2978 6459 3.492137 GGGAAGCATTGCATCTCCATTTC 60.492 47.826 19.81 9.53 38.65 2.17
2979 6460 3.492137 GGAAGCATTGCATCTCCATTTCC 60.492 47.826 11.91 8.64 35.98 3.13
2980 6461 1.679680 AGCATTGCATCTCCATTTCCG 59.320 47.619 11.91 0.00 0.00 4.30
2982 6463 0.664761 ATTGCATCTCCATTTCCGCG 59.335 50.000 0.00 0.00 0.00 6.46
2983 6464 1.992233 TTGCATCTCCATTTCCGCGC 61.992 55.000 0.00 0.00 0.00 6.86
2988 6473 1.153568 CTCCATTTCCGCGCTCTCA 60.154 57.895 5.56 0.00 0.00 3.27
3002 6487 1.416813 CTCTCACGCTCCGTTGCATC 61.417 60.000 0.00 0.00 38.32 3.91
3039 6525 4.331168 GACATTCGTCATAAAGCTCAGCTT 59.669 41.667 5.91 5.91 45.45 3.74
3076 6562 1.481363 GCCTCCTACCTAGGTTGTCAC 59.519 57.143 22.11 3.58 44.02 3.67
3077 6563 2.108970 CCTCCTACCTAGGTTGTCACC 58.891 57.143 22.11 0.00 44.02 4.02
3097 6583 2.202756 CGGTTGCGCCTCTACCTC 60.203 66.667 4.18 0.00 38.26 3.85
3098 6584 2.978824 GGTTGCGCCTCTACCTCA 59.021 61.111 4.18 0.00 37.56 3.86
3100 6586 0.107654 GGTTGCGCCTCTACCTCATT 60.108 55.000 4.18 0.00 37.56 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.727627 GTTTATTTTTGGTGCAATTTTCATCAA 57.272 25.926 0.00 0.34 33.19 2.57
6 7 8.896744 TGTTTATTTTTGGTGCAATTTTCATCA 58.103 25.926 0.00 0.00 0.00 3.07
7 8 9.727627 TTGTTTATTTTTGGTGCAATTTTCATC 57.272 25.926 0.00 0.00 0.00 2.92
8 9 9.513727 GTTGTTTATTTTTGGTGCAATTTTCAT 57.486 25.926 0.00 0.00 0.00 2.57
9 10 8.734386 AGTTGTTTATTTTTGGTGCAATTTTCA 58.266 25.926 0.00 0.00 0.00 2.69
10 11 9.008289 CAGTTGTTTATTTTTGGTGCAATTTTC 57.992 29.630 0.00 0.00 0.00 2.29
11 12 7.487509 GCAGTTGTTTATTTTTGGTGCAATTTT 59.512 29.630 0.00 0.00 0.00 1.82
12 13 6.971756 GCAGTTGTTTATTTTTGGTGCAATTT 59.028 30.769 0.00 0.00 0.00 1.82
13 14 6.459435 GGCAGTTGTTTATTTTTGGTGCAATT 60.459 34.615 0.00 0.00 0.00 2.32
14 15 5.008514 GGCAGTTGTTTATTTTTGGTGCAAT 59.991 36.000 0.00 0.00 0.00 3.56
15 16 4.333926 GGCAGTTGTTTATTTTTGGTGCAA 59.666 37.500 0.00 0.00 0.00 4.08
16 17 3.873952 GGCAGTTGTTTATTTTTGGTGCA 59.126 39.130 0.00 0.00 0.00 4.57
17 18 3.873952 TGGCAGTTGTTTATTTTTGGTGC 59.126 39.130 0.00 0.00 0.00 5.01
18 19 5.526846 ACATGGCAGTTGTTTATTTTTGGTG 59.473 36.000 0.00 0.00 0.00 4.17
19 20 5.679601 ACATGGCAGTTGTTTATTTTTGGT 58.320 33.333 0.00 0.00 0.00 3.67
20 21 6.616774 AACATGGCAGTTGTTTATTTTTGG 57.383 33.333 0.70 0.00 33.64 3.28
21 22 8.908172 AAAAACATGGCAGTTGTTTATTTTTG 57.092 26.923 16.98 0.00 44.32 2.44
53 54 2.046023 TGCGAACCTGCCAGATGG 60.046 61.111 0.00 0.00 38.53 3.51
54 55 1.078918 TCTGCGAACCTGCCAGATG 60.079 57.895 0.00 0.00 0.00 2.90
55 56 1.220206 CTCTGCGAACCTGCCAGAT 59.780 57.895 0.00 0.00 0.00 2.90
56 57 2.659016 CTCTGCGAACCTGCCAGA 59.341 61.111 0.00 0.00 0.00 3.86
57 58 2.435586 CCTCTGCGAACCTGCCAG 60.436 66.667 0.00 0.00 0.00 4.85
58 59 3.240134 GACCTCTGCGAACCTGCCA 62.240 63.158 0.00 0.00 0.00 4.92
59 60 2.435059 GACCTCTGCGAACCTGCC 60.435 66.667 0.00 0.00 0.00 4.85
60 61 1.078848 ATGACCTCTGCGAACCTGC 60.079 57.895 0.00 0.00 0.00 4.85
61 62 1.364626 GCATGACCTCTGCGAACCTG 61.365 60.000 0.00 0.00 0.00 4.00
62 63 1.078848 GCATGACCTCTGCGAACCT 60.079 57.895 0.00 0.00 0.00 3.50
63 64 3.490890 GCATGACCTCTGCGAACC 58.509 61.111 0.00 0.00 0.00 3.62
68 69 1.357258 CTGACACGCATGACCTCTGC 61.357 60.000 0.00 0.00 36.26 4.26
69 70 1.357258 GCTGACACGCATGACCTCTG 61.357 60.000 0.00 0.00 0.00 3.35
70 71 1.079543 GCTGACACGCATGACCTCT 60.080 57.895 0.00 0.00 0.00 3.69
71 72 0.173481 TAGCTGACACGCATGACCTC 59.827 55.000 0.00 0.00 0.00 3.85
72 73 0.608130 TTAGCTGACACGCATGACCT 59.392 50.000 0.00 0.00 0.00 3.85
73 74 0.721718 GTTAGCTGACACGCATGACC 59.278 55.000 3.32 0.00 0.00 4.02
74 75 0.366871 CGTTAGCTGACACGCATGAC 59.633 55.000 9.54 0.00 0.00 3.06
75 76 0.038618 ACGTTAGCTGACACGCATGA 60.039 50.000 9.54 0.00 40.16 3.07
76 77 0.790207 AACGTTAGCTGACACGCATG 59.210 50.000 9.54 0.00 40.16 4.06
77 78 1.068474 GAACGTTAGCTGACACGCAT 58.932 50.000 9.54 2.09 40.16 4.73
78 79 0.249114 TGAACGTTAGCTGACACGCA 60.249 50.000 9.54 0.16 40.16 5.24
79 80 0.161024 GTGAACGTTAGCTGACACGC 59.839 55.000 9.54 2.85 40.16 5.34
80 81 1.452025 CAGTGAACGTTAGCTGACACG 59.548 52.381 20.48 10.91 42.29 4.49
81 82 1.792949 CCAGTGAACGTTAGCTGACAC 59.207 52.381 24.47 16.78 0.00 3.67
82 83 1.270094 CCCAGTGAACGTTAGCTGACA 60.270 52.381 24.47 7.01 0.00 3.58
83 84 1.429463 CCCAGTGAACGTTAGCTGAC 58.571 55.000 24.47 0.00 0.00 3.51
84 85 0.320374 CCCCAGTGAACGTTAGCTGA 59.680 55.000 24.47 0.00 0.00 4.26
85 86 0.320374 TCCCCAGTGAACGTTAGCTG 59.680 55.000 18.99 18.99 0.00 4.24
86 87 0.320697 GTCCCCAGTGAACGTTAGCT 59.679 55.000 0.00 0.00 0.00 3.32
87 88 0.320697 AGTCCCCAGTGAACGTTAGC 59.679 55.000 0.00 0.00 0.00 3.09
88 89 1.337823 CCAGTCCCCAGTGAACGTTAG 60.338 57.143 0.00 0.00 0.00 2.34
89 90 0.682852 CCAGTCCCCAGTGAACGTTA 59.317 55.000 0.00 0.00 0.00 3.18
90 91 1.450211 CCAGTCCCCAGTGAACGTT 59.550 57.895 0.00 0.00 0.00 3.99
91 92 2.516888 CCCAGTCCCCAGTGAACGT 61.517 63.158 0.00 0.00 0.00 3.99
92 93 1.189524 TACCCAGTCCCCAGTGAACG 61.190 60.000 0.00 0.00 0.00 3.95
93 94 1.286248 ATACCCAGTCCCCAGTGAAC 58.714 55.000 0.00 0.00 0.00 3.18
94 95 2.053747 AATACCCAGTCCCCAGTGAA 57.946 50.000 0.00 0.00 0.00 3.18
95 96 2.759355 CTAATACCCAGTCCCCAGTGA 58.241 52.381 0.00 0.00 0.00 3.41
96 97 1.141053 GCTAATACCCAGTCCCCAGTG 59.859 57.143 0.00 0.00 0.00 3.66
97 98 1.508256 GCTAATACCCAGTCCCCAGT 58.492 55.000 0.00 0.00 0.00 4.00
98 99 0.393077 CGCTAATACCCAGTCCCCAG 59.607 60.000 0.00 0.00 0.00 4.45
99 100 0.325860 ACGCTAATACCCAGTCCCCA 60.326 55.000 0.00 0.00 0.00 4.96
100 101 0.391966 GACGCTAATACCCAGTCCCC 59.608 60.000 0.00 0.00 0.00 4.81
101 102 0.031721 CGACGCTAATACCCAGTCCC 59.968 60.000 0.00 0.00 0.00 4.46
102 103 0.743097 ACGACGCTAATACCCAGTCC 59.257 55.000 0.00 0.00 0.00 3.85
103 104 2.573941 AACGACGCTAATACCCAGTC 57.426 50.000 0.00 0.00 0.00 3.51
104 105 4.660789 ATTAACGACGCTAATACCCAGT 57.339 40.909 1.74 0.00 0.00 4.00
105 106 6.441274 TCTAATTAACGACGCTAATACCCAG 58.559 40.000 4.06 1.36 0.00 4.45
106 107 6.389830 TCTAATTAACGACGCTAATACCCA 57.610 37.500 4.06 0.00 0.00 4.51
107 108 5.860716 CCTCTAATTAACGACGCTAATACCC 59.139 44.000 4.06 0.00 0.00 3.69
108 109 5.860716 CCCTCTAATTAACGACGCTAATACC 59.139 44.000 4.06 0.00 0.00 2.73
109 110 6.442112 ACCCTCTAATTAACGACGCTAATAC 58.558 40.000 4.06 0.00 0.00 1.89
110 111 6.639632 ACCCTCTAATTAACGACGCTAATA 57.360 37.500 4.06 0.00 0.00 0.98
111 112 5.526506 ACCCTCTAATTAACGACGCTAAT 57.473 39.130 0.00 0.00 0.00 1.73
112 113 4.989279 ACCCTCTAATTAACGACGCTAA 57.011 40.909 0.00 0.00 0.00 3.09
113 114 4.496341 CGAACCCTCTAATTAACGACGCTA 60.496 45.833 0.00 0.00 0.00 4.26
114 115 3.733077 CGAACCCTCTAATTAACGACGCT 60.733 47.826 0.00 0.00 0.00 5.07
115 116 2.533129 CGAACCCTCTAATTAACGACGC 59.467 50.000 0.00 0.00 0.00 5.19
116 117 4.019919 TCGAACCCTCTAATTAACGACG 57.980 45.455 0.00 0.00 0.00 5.12
117 118 5.346522 ACATCGAACCCTCTAATTAACGAC 58.653 41.667 0.00 0.00 0.00 4.34
118 119 5.587388 ACATCGAACCCTCTAATTAACGA 57.413 39.130 0.00 0.00 0.00 3.85
119 120 6.501781 ACTACATCGAACCCTCTAATTAACG 58.498 40.000 0.00 0.00 0.00 3.18
120 121 7.714703 AGACTACATCGAACCCTCTAATTAAC 58.285 38.462 0.00 0.00 0.00 2.01
121 122 7.893124 AGACTACATCGAACCCTCTAATTAA 57.107 36.000 0.00 0.00 0.00 1.40
122 123 7.893124 AAGACTACATCGAACCCTCTAATTA 57.107 36.000 0.00 0.00 0.00 1.40
123 124 6.793505 AAGACTACATCGAACCCTCTAATT 57.206 37.500 0.00 0.00 0.00 1.40
124 125 6.793505 AAAGACTACATCGAACCCTCTAAT 57.206 37.500 0.00 0.00 0.00 1.73
125 126 7.201884 CCATAAAGACTACATCGAACCCTCTAA 60.202 40.741 0.00 0.00 0.00 2.10
126 127 6.264744 CCATAAAGACTACATCGAACCCTCTA 59.735 42.308 0.00 0.00 0.00 2.43
127 128 5.069251 CCATAAAGACTACATCGAACCCTCT 59.931 44.000 0.00 0.00 0.00 3.69
128 129 5.290386 CCATAAAGACTACATCGAACCCTC 58.710 45.833 0.00 0.00 0.00 4.30
129 130 4.443034 GCCATAAAGACTACATCGAACCCT 60.443 45.833 0.00 0.00 0.00 4.34
130 131 3.808174 GCCATAAAGACTACATCGAACCC 59.192 47.826 0.00 0.00 0.00 4.11
131 132 4.439057 TGCCATAAAGACTACATCGAACC 58.561 43.478 0.00 0.00 0.00 3.62
132 133 6.417191 TTTGCCATAAAGACTACATCGAAC 57.583 37.500 0.00 0.00 0.00 3.95
133 134 7.624360 ATTTTGCCATAAAGACTACATCGAA 57.376 32.000 0.00 0.00 0.00 3.71
134 135 8.725405 TTATTTTGCCATAAAGACTACATCGA 57.275 30.769 0.00 0.00 0.00 3.59
135 136 9.781834 TTTTATTTTGCCATAAAGACTACATCG 57.218 29.630 0.00 0.00 31.67 3.84
160 161 5.539955 ACATGGCCTTTAATTGTTGAGACTT 59.460 36.000 3.32 0.00 0.00 3.01
162 163 5.183904 AGACATGGCCTTTAATTGTTGAGAC 59.816 40.000 3.32 0.00 0.00 3.36
163 164 5.324409 AGACATGGCCTTTAATTGTTGAGA 58.676 37.500 3.32 0.00 0.00 3.27
227 229 6.073222 ACACCAAGTTCAATAAGCGAAGTAAG 60.073 38.462 0.00 0.00 0.00 2.34
234 236 2.031245 TGCACACCAAGTTCAATAAGCG 60.031 45.455 0.00 0.00 0.00 4.68
316 319 1.928503 CTGCAAAACCACACAAGCTTG 59.071 47.619 24.84 24.84 0.00 4.01
319 322 0.179103 AGCTGCAAAACCACACAAGC 60.179 50.000 1.02 0.00 0.00 4.01
325 342 2.480037 GGCAAATAAGCTGCAAAACCAC 59.520 45.455 1.02 0.00 41.78 4.16
331 348 4.397730 TCTTAATCGGCAAATAAGCTGCAA 59.602 37.500 1.02 0.00 41.78 4.08
360 377 9.639601 CTACAAACATCTTACTCATGTAACTCA 57.360 33.333 0.00 0.00 33.12 3.41
391 414 1.787155 GTCGTATGCCGCTACAATCAG 59.213 52.381 0.00 0.00 36.19 2.90
402 425 2.161410 TCACAGCAATTTGTCGTATGCC 59.839 45.455 0.00 0.00 39.59 4.40
412 435 4.405116 AAACCATGTGTCACAGCAATTT 57.595 36.364 12.03 6.63 0.00 1.82
420 443 7.971722 GGGTGTTATTATAAAACCATGTGTCAC 59.028 37.037 21.84 6.57 32.28 3.67
422 445 8.288689 AGGGTGTTATTATAAAACCATGTGTC 57.711 34.615 21.84 7.12 32.28 3.67
516 540 2.613133 GAGCAGCACTGAAATCAGATCC 59.387 50.000 16.93 4.88 46.59 3.36
547 571 2.563976 CAGCACAAAGACGAAATCACG 58.436 47.619 0.00 0.00 39.31 4.35
601 625 0.670162 GCGCTTCATGTGCCCATATT 59.330 50.000 0.00 0.00 45.73 1.28
649 673 2.604855 CCGCGGTAGTTACTCATAGCTG 60.605 54.545 19.50 0.00 0.00 4.24
656 680 1.988467 GTGAAACCGCGGTAGTTACTC 59.012 52.381 34.44 20.03 0.00 2.59
707 738 2.556287 CAGACGGCGGCAAGAAAC 59.444 61.111 18.30 0.00 0.00 2.78
746 777 4.319115 GCACGTACGTGGTGAATATATACG 59.681 45.833 40.17 17.27 45.49 3.06
748 779 5.214417 GTGCACGTACGTGGTGAATATATA 58.786 41.667 40.17 0.09 45.49 0.86
749 780 4.046462 GTGCACGTACGTGGTGAATATAT 58.954 43.478 40.17 5.67 45.49 0.86
908 3115 1.746991 GCTTGGGGAAGAAGGAGCG 60.747 63.158 0.00 0.00 0.00 5.03
990 3202 1.074850 AGTTGGGTTTGGGTTGGGG 60.075 57.895 0.00 0.00 0.00 4.96
991 3203 1.118965 GGAGTTGGGTTTGGGTTGGG 61.119 60.000 0.00 0.00 0.00 4.12
992 3204 0.397816 TGGAGTTGGGTTTGGGTTGG 60.398 55.000 0.00 0.00 0.00 3.77
993 3205 1.618343 GATGGAGTTGGGTTTGGGTTG 59.382 52.381 0.00 0.00 0.00 3.77
994 3206 1.821666 CGATGGAGTTGGGTTTGGGTT 60.822 52.381 0.00 0.00 0.00 4.11
995 3207 0.251165 CGATGGAGTTGGGTTTGGGT 60.251 55.000 0.00 0.00 0.00 4.51
996 3208 1.595093 GCGATGGAGTTGGGTTTGGG 61.595 60.000 0.00 0.00 0.00 4.12
997 3209 1.595093 GGCGATGGAGTTGGGTTTGG 61.595 60.000 0.00 0.00 0.00 3.28
998 3210 0.893270 TGGCGATGGAGTTGGGTTTG 60.893 55.000 0.00 0.00 0.00 2.93
999 3211 0.039618 ATGGCGATGGAGTTGGGTTT 59.960 50.000 0.00 0.00 0.00 3.27
1000 3212 0.394352 GATGGCGATGGAGTTGGGTT 60.394 55.000 0.00 0.00 0.00 4.11
1001 3213 1.224592 GATGGCGATGGAGTTGGGT 59.775 57.895 0.00 0.00 0.00 4.51
1030 3242 4.412796 TGTGAGAGGAGGAATGCTATTG 57.587 45.455 0.00 0.00 0.00 1.90
1031 3243 5.843421 AGTATGTGAGAGGAGGAATGCTATT 59.157 40.000 0.00 0.00 0.00 1.73
1032 3244 5.401750 AGTATGTGAGAGGAGGAATGCTAT 58.598 41.667 0.00 0.00 0.00 2.97
1033 3245 4.809193 AGTATGTGAGAGGAGGAATGCTA 58.191 43.478 0.00 0.00 0.00 3.49
1034 3246 3.640967 GAGTATGTGAGAGGAGGAATGCT 59.359 47.826 0.00 0.00 0.00 3.79
1035 3247 3.244044 GGAGTATGTGAGAGGAGGAATGC 60.244 52.174 0.00 0.00 0.00 3.56
1045 3257 1.560505 TGCTGCTGGAGTATGTGAGA 58.439 50.000 0.00 0.00 0.00 3.27
1099 3332 2.435059 GGAAGAGCTGGTGCCGTC 60.435 66.667 0.00 0.00 40.80 4.79
1113 3346 6.938507 ACGTGTTAGTGTATATTTGAGGGAA 58.061 36.000 0.00 0.00 0.00 3.97
1114 3347 6.534475 ACGTGTTAGTGTATATTTGAGGGA 57.466 37.500 0.00 0.00 0.00 4.20
1558 3791 2.876645 GCGAACACGAGCGGAGAG 60.877 66.667 0.00 0.00 0.00 3.20
1672 3905 3.127533 GCGAACCTCGGCTGCATT 61.128 61.111 0.50 0.00 40.84 3.56
1733 3974 2.883828 ATGGGTCGATCCATCCGCC 61.884 63.158 24.95 0.00 43.57 6.13
1828 4069 2.045536 CCCACCTGCCTTGCTCTC 60.046 66.667 0.00 0.00 0.00 3.20
1838 4079 0.734889 GCGACATCAATTCCCACCTG 59.265 55.000 0.00 0.00 0.00 4.00
2040 4281 4.851558 ACTAACGCGATCAAAATTTTGCTC 59.148 37.500 23.36 21.54 38.05 4.26
2042 4283 5.116377 TCAACTAACGCGATCAAAATTTTGC 59.884 36.000 23.36 12.43 38.05 3.68
2129 4371 1.778591 CGCACGTTTAGGCAAAAGTTG 59.221 47.619 0.00 0.00 34.65 3.16
2132 4374 0.040425 AGCGCACGTTTAGGCAAAAG 60.040 50.000 11.47 0.00 0.00 2.27
2238 4566 9.734984 AATGGCAAATGTTTAGTACTACTAGTT 57.265 29.630 0.00 0.00 31.47 2.24
2239 4567 9.734984 AAATGGCAAATGTTTAGTACTACTAGT 57.265 29.630 0.91 0.00 31.47 2.57
2241 4569 9.953565 AGAAATGGCAAATGTTTAGTACTACTA 57.046 29.630 0.91 0.00 0.00 1.82
2242 4570 8.863872 AGAAATGGCAAATGTTTAGTACTACT 57.136 30.769 0.91 0.00 0.00 2.57
2245 4573 9.461312 TCATAGAAATGGCAAATGTTTAGTACT 57.539 29.630 0.00 0.00 33.61 2.73
2267 4595 6.765989 GTGTGTACATGAAGCCCTTAATCATA 59.234 38.462 0.00 0.00 32.73 2.15
2270 4598 4.034048 CGTGTGTACATGAAGCCCTTAATC 59.966 45.833 0.00 0.00 34.90 1.75
2289 4617 3.967203 TTTTAACTAAAAGCGCCGTGT 57.033 38.095 2.29 0.00 32.00 4.49
2346 4674 1.398451 CGAACACAGAAACACATCGGC 60.398 52.381 0.00 0.00 0.00 5.54
2347 4675 2.131972 TCGAACACAGAAACACATCGG 58.868 47.619 0.00 0.00 0.00 4.18
2348 4676 3.675225 AGATCGAACACAGAAACACATCG 59.325 43.478 0.00 0.00 0.00 3.84
2349 4677 4.686091 TCAGATCGAACACAGAAACACATC 59.314 41.667 0.00 0.00 0.00 3.06
2350 4678 4.631131 TCAGATCGAACACAGAAACACAT 58.369 39.130 0.00 0.00 0.00 3.21
2351 4679 4.053469 TCAGATCGAACACAGAAACACA 57.947 40.909 0.00 0.00 0.00 3.72
2415 4743 1.405933 GGGTTTAATCTACACGGCCGT 60.406 52.381 28.70 28.70 0.00 5.68
2419 4747 0.925466 CGCGGGTTTAATCTACACGG 59.075 55.000 0.00 0.00 42.45 4.94
2442 4770 4.155285 GTAAGTATACATGAGCCGTCGGC 61.155 52.174 29.07 29.07 39.34 5.54
2443 4771 2.795175 AAGTATACATGAGCCGTCGG 57.205 50.000 6.99 6.99 0.00 4.79
2444 4772 4.219802 CAGTAAGTATACATGAGCCGTCG 58.780 47.826 5.50 0.00 34.29 5.12
2445 4773 4.976731 CACAGTAAGTATACATGAGCCGTC 59.023 45.833 5.50 0.00 34.29 4.79
2446 4774 4.643334 TCACAGTAAGTATACATGAGCCGT 59.357 41.667 5.50 0.00 34.29 5.68
2453 4781 4.595116 GACGCGTCACAGTAAGTATACAT 58.405 43.478 33.09 0.00 34.29 2.29
2499 4985 6.183361 TGCCCTCCATGTCTAAACAAATTTTT 60.183 34.615 0.00 0.00 39.30 1.94
2500 4986 5.306678 TGCCCTCCATGTCTAAACAAATTTT 59.693 36.000 0.00 0.00 39.30 1.82
2501 4987 4.837860 TGCCCTCCATGTCTAAACAAATTT 59.162 37.500 0.00 0.00 39.30 1.82
2502 4988 4.415596 TGCCCTCCATGTCTAAACAAATT 58.584 39.130 0.00 0.00 39.30 1.82
2503 4989 4.046286 TGCCCTCCATGTCTAAACAAAT 57.954 40.909 0.00 0.00 39.30 2.32
2511 4997 2.242043 CAAACTTTGCCCTCCATGTCT 58.758 47.619 0.00 0.00 0.00 3.41
2536 5022 1.658994 AAGTTGACCTTGAAACGCGA 58.341 45.000 15.93 0.00 30.18 5.87
2642 5159 1.355720 AGGCCAATTAAGTGGAGCAGT 59.644 47.619 25.51 1.45 41.65 4.40
2645 5162 0.457443 GCAGGCCAATTAAGTGGAGC 59.543 55.000 25.51 19.62 41.65 4.70
2683 5200 4.686191 TGGGGAAAGAACGTTACAGTAA 57.314 40.909 0.00 0.00 0.00 2.24
2684 5201 4.895668 ATGGGGAAAGAACGTTACAGTA 57.104 40.909 0.00 0.00 0.00 2.74
2732 5779 6.412072 GGTATGAACAACACTATACGTACGAC 59.588 42.308 24.41 2.66 0.00 4.34
2744 6225 5.944007 AGAGGGTATTTGGTATGAACAACAC 59.056 40.000 0.00 0.00 0.00 3.32
2781 6262 9.774742 GTTGTTGATGTTTGGAATACTCTTATC 57.225 33.333 0.00 0.00 0.00 1.75
2785 6266 7.425606 GTTGTTGTTGATGTTTGGAATACTCT 58.574 34.615 0.00 0.00 0.00 3.24
2792 6273 3.692101 ACTCGTTGTTGTTGATGTTTGGA 59.308 39.130 0.00 0.00 0.00 3.53
2800 6281 4.395959 ACTTCCTACTCGTTGTTGTTGA 57.604 40.909 0.00 0.00 0.00 3.18
2817 6298 7.173390 AGGTATGCTTAGTTCACAGAAAACTTC 59.827 37.037 0.00 0.00 38.00 3.01
2820 6301 6.426937 TGAGGTATGCTTAGTTCACAGAAAAC 59.573 38.462 0.00 0.00 0.00 2.43
2826 6307 5.395657 CCATCTGAGGTATGCTTAGTTCACA 60.396 44.000 0.00 0.00 0.00 3.58
2828 6309 4.716784 ACCATCTGAGGTATGCTTAGTTCA 59.283 41.667 0.00 0.00 40.98 3.18
2841 6322 6.409704 TCACAAAGAATCTAACCATCTGAGG 58.590 40.000 0.00 0.00 0.00 3.86
2853 6334 5.420104 GGGTTGATTCCATCACAAAGAATCT 59.580 40.000 11.87 0.00 44.02 2.40
2865 6346 2.718609 CCTCCCTATGGGTTGATTCCAT 59.281 50.000 2.25 0.00 44.74 3.41
2879 6360 0.551879 CGTCCTTCCTCTCCTCCCTA 59.448 60.000 0.00 0.00 0.00 3.53
2880 6361 1.215679 TCGTCCTTCCTCTCCTCCCT 61.216 60.000 0.00 0.00 0.00 4.20
2881 6362 0.753848 CTCGTCCTTCCTCTCCTCCC 60.754 65.000 0.00 0.00 0.00 4.30
2882 6363 1.388837 GCTCGTCCTTCCTCTCCTCC 61.389 65.000 0.00 0.00 0.00 4.30
2883 6364 1.720694 CGCTCGTCCTTCCTCTCCTC 61.721 65.000 0.00 0.00 0.00 3.71
2918 6399 4.394712 GGCGTCCACACCTCCTGG 62.395 72.222 0.00 0.00 39.83 4.45
2954 6435 1.030457 GGAGATGCAATGCTTCCCAG 58.970 55.000 16.09 0.00 33.95 4.45
2955 6436 0.332293 TGGAGATGCAATGCTTCCCA 59.668 50.000 19.51 19.51 33.95 4.37
2964 6445 1.992233 GCGCGGAAATGGAGATGCAA 61.992 55.000 8.83 0.00 0.00 4.08
2982 6463 3.482783 GCAACGGAGCGTGAGAGC 61.483 66.667 0.00 0.00 39.99 4.09
2983 6464 1.416813 GATGCAACGGAGCGTGAGAG 61.417 60.000 0.00 0.00 39.99 3.20
3005 6491 1.580893 CGAATGTCGTGGCGCATTG 60.581 57.895 10.83 0.00 35.27 2.82
3015 6501 5.493353 AGCTGAGCTTTATGACGAATGTCG 61.493 45.833 0.00 0.00 41.63 4.35
3026 6512 9.416430 GACACAATTGTCGAAGCTGAGCTTTAT 62.416 40.741 21.95 0.00 44.79 1.40
3027 6513 8.201909 GACACAATTGTCGAAGCTGAGCTTTA 62.202 42.308 21.95 10.03 44.79 1.85
3042 6528 1.076024 AGGAGGCATGGACACAATTGT 59.924 47.619 4.92 4.92 39.32 2.71
3044 6530 2.357154 GGTAGGAGGCATGGACACAATT 60.357 50.000 0.00 0.00 0.00 2.32
3045 6531 1.212935 GGTAGGAGGCATGGACACAAT 59.787 52.381 0.00 0.00 0.00 2.71
3077 6563 2.202756 GTAGAGGCGCAACCGGAG 60.203 66.667 9.46 0.15 46.52 4.63
3097 6583 0.371645 GGCGAGTTCGAGCTCAAATG 59.628 55.000 26.02 12.64 43.02 2.32
3098 6584 0.741221 GGGCGAGTTCGAGCTCAAAT 60.741 55.000 26.02 6.55 43.02 2.32
3100 6586 2.261671 GGGCGAGTTCGAGCTCAA 59.738 61.111 26.02 4.52 43.02 3.02


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

AutoCloner maintained by Alex Coulton.