Multiple sequence alignment - TraesCS1D01G118700

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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 TraesCS1D01G118700 chr1D 100.000 3647 0 0 1 3647 114366886 114363240 0.000000e+00 6735.0
1 TraesCS1D01G118700 chr1D 82.812 2304 307 53 829 3103 381973779 381976022 0.000000e+00 1978.0
2 TraesCS1D01G118700 chr1D 86.598 97 7 4 494 590 112467923 112467833 6.440000e-18 102.0
3 TraesCS1D01G118700 chr1D 97.143 35 1 0 416 450 375972003 375971969 3.930000e-05 60.2
4 TraesCS1D01G118700 chr1A 96.258 2993 94 12 656 3647 124898074 124895099 0.000000e+00 4891.0
5 TraesCS1D01G118700 chr1A 83.355 2295 301 47 829 3097 482248456 482250695 0.000000e+00 2047.0
6 TraesCS1D01G118700 chr1B 97.940 2427 49 1 857 3282 175429799 175427373 0.000000e+00 4204.0
7 TraesCS1D01G118700 chr1B 82.872 2277 310 41 829 3073 511973110 511975338 0.000000e+00 1971.0
8 TraesCS1D01G118700 chr1B 92.573 377 6 3 3278 3647 175425177 175424816 4.170000e-144 521.0
9 TraesCS1D01G118700 chr1B 90.000 70 5 2 3243 3311 433438979 433438911 5.020000e-14 89.8
10 TraesCS1D01G118700 chr5D 82.299 1627 252 23 885 2484 40929133 40927516 0.000000e+00 1376.0
11 TraesCS1D01G118700 chr5D 95.714 70 3 0 489 558 461429822 461429753 2.980000e-21 113.0
12 TraesCS1D01G118700 chr5D 97.778 45 1 0 556 600 545227794 545227838 1.090000e-10 78.7
13 TraesCS1D01G118700 chr5D 97.778 45 1 0 556 600 554927675 554927719 1.090000e-10 78.7
14 TraesCS1D01G118700 chr3B 94.118 102 4 1 498 597 241678780 241678881 1.750000e-33 154.0
15 TraesCS1D01G118700 chr2B 88.785 107 11 1 494 600 615778421 615778316 2.960000e-26 130.0
16 TraesCS1D01G118700 chr6A 77.011 261 37 18 250 501 63115892 63115646 1.060000e-25 128.0
17 TraesCS1D01G118700 chr2D 98.462 65 1 0 494 558 79387433 79387369 8.280000e-22 115.0
18 TraesCS1D01G118700 chr2D 92.208 77 4 1 484 558 341665960 341665884 1.380000e-19 108.0
19 TraesCS1D01G118700 chr7D 97.015 67 1 1 493 558 519264636 519264570 1.070000e-20 111.0
20 TraesCS1D01G118700 chr7D 86.316 95 9 1 496 590 60339113 60339023 2.320000e-17 100.0
21 TraesCS1D01G118700 chr7D 97.778 45 1 0 556 600 448931323 448931367 1.090000e-10 78.7
22 TraesCS1D01G118700 chr7D 97.778 45 1 0 556 600 494673601 494673645 1.090000e-10 78.7
23 TraesCS1D01G118700 chr4D 95.652 69 3 0 490 558 403409523 403409591 1.070000e-20 111.0
24 TraesCS1D01G118700 chr7B 87.654 81 8 2 498 576 653977492 653977572 3.880000e-15 93.5
25 TraesCS1D01G118700 chr6B 76.744 172 23 10 336 505 588312454 588312298 3.020000e-11 80.5
26 TraesCS1D01G118700 chr5A 82.105 95 11 3 495 583 397248757 397248851 3.910000e-10 76.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G118700 chr1D 114363240 114366886 3646 True 6735.0 6735 100.0000 1 3647 1 chr1D.!!$R2 3646
1 TraesCS1D01G118700 chr1D 381973779 381976022 2243 False 1978.0 1978 82.8120 829 3103 1 chr1D.!!$F1 2274
2 TraesCS1D01G118700 chr1A 124895099 124898074 2975 True 4891.0 4891 96.2580 656 3647 1 chr1A.!!$R1 2991
3 TraesCS1D01G118700 chr1A 482248456 482250695 2239 False 2047.0 2047 83.3550 829 3097 1 chr1A.!!$F1 2268
4 TraesCS1D01G118700 chr1B 175424816 175429799 4983 True 2362.5 4204 95.2565 857 3647 2 chr1B.!!$R2 2790
5 TraesCS1D01G118700 chr1B 511973110 511975338 2228 False 1971.0 1971 82.8720 829 3073 1 chr1B.!!$F1 2244
6 TraesCS1D01G118700 chr5D 40927516 40929133 1617 True 1376.0 1376 82.2990 885 2484 1 chr5D.!!$R1 1599

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
30 31 0.039618 AACATGGGTTTGGCCGATCT 59.960 50.0 0.00 0.0 38.44 2.75 F
31 32 0.039618 ACATGGGTTTGGCCGATCTT 59.960 50.0 0.00 0.0 38.44 2.40 F
562 563 0.041576 GTGTCAAAAACGCTCCGTCC 60.042 55.0 0.00 0.0 39.99 4.79 F
722 723 0.246635 GGCTCTCCTTCTGTAACGCA 59.753 55.0 0.00 0.0 0.00 5.24 F
820 821 0.249120 GGCATGCCCAAAAGGGTTAC 59.751 55.0 27.24 0.0 35.41 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1674 1.376609 CTTCACGGCAATACCCCTGC 61.377 60.000 0.00 0.0 39.16 4.85 R
1951 2002 3.201487 TCATGAATCCTCTTGTCATGGCT 59.799 43.478 11.74 0.0 45.67 4.75 R
2315 2369 2.842496 ACTTCATCTGGAGCAATCCTCA 59.158 45.455 0.00 0.0 42.62 3.86 R
2637 2697 1.972872 AGGGTTCAGTTCACTGCTTG 58.027 50.000 1.74 0.0 43.46 4.01 R
2676 2736 6.875076 AGAGTACGCTACCTTCAATTATTGT 58.125 36.000 4.77 0.0 0.00 2.71 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 3.281240 GGTGCTCAGCCAACATGG 58.719 61.111 0.00 0.00 41.55 3.66
18 19 2.345760 GGTGCTCAGCCAACATGGG 61.346 63.158 0.00 0.00 38.19 4.00
25 26 2.347114 GCCAACATGGGTTTGGCC 59.653 61.111 22.07 0.00 41.40 5.36
26 27 2.656055 CCAACATGGGTTTGGCCG 59.344 61.111 0.00 0.00 38.44 6.13
27 28 1.905843 CCAACATGGGTTTGGCCGA 60.906 57.895 0.00 0.00 38.44 5.54
28 29 1.257055 CCAACATGGGTTTGGCCGAT 61.257 55.000 0.00 0.00 38.44 4.18
29 30 0.173255 CAACATGGGTTTGGCCGATC 59.827 55.000 0.00 0.00 38.44 3.69
30 31 0.039618 AACATGGGTTTGGCCGATCT 59.960 50.000 0.00 0.00 38.44 2.75
31 32 0.039618 ACATGGGTTTGGCCGATCTT 59.960 50.000 0.00 0.00 38.44 2.40
32 33 1.185315 CATGGGTTTGGCCGATCTTT 58.815 50.000 0.00 0.00 38.44 2.52
33 34 2.291282 ACATGGGTTTGGCCGATCTTTA 60.291 45.455 0.00 0.00 38.44 1.85
34 35 2.818751 TGGGTTTGGCCGATCTTTAT 57.181 45.000 0.00 0.00 38.44 1.40
35 36 2.650322 TGGGTTTGGCCGATCTTTATC 58.350 47.619 0.00 0.00 38.44 1.75
36 37 1.954382 GGGTTTGGCCGATCTTTATCC 59.046 52.381 0.00 0.00 38.44 2.59
37 38 2.650322 GGTTTGGCCGATCTTTATCCA 58.350 47.619 0.00 0.00 0.00 3.41
38 39 2.357952 GGTTTGGCCGATCTTTATCCAC 59.642 50.000 0.00 0.00 0.00 4.02
39 40 3.013921 GTTTGGCCGATCTTTATCCACA 58.986 45.455 0.00 0.00 0.00 4.17
40 41 3.358111 TTGGCCGATCTTTATCCACAA 57.642 42.857 0.00 0.00 0.00 3.33
41 42 2.917933 TGGCCGATCTTTATCCACAAG 58.082 47.619 0.00 0.00 0.00 3.16
42 43 2.222027 GGCCGATCTTTATCCACAAGG 58.778 52.381 0.00 0.00 0.00 3.61
43 44 1.604278 GCCGATCTTTATCCACAAGGC 59.396 52.381 0.00 0.00 35.00 4.35
44 45 2.746472 GCCGATCTTTATCCACAAGGCT 60.746 50.000 0.00 0.00 39.01 4.58
45 46 3.494398 GCCGATCTTTATCCACAAGGCTA 60.494 47.826 0.00 0.00 39.01 3.93
46 47 4.804261 GCCGATCTTTATCCACAAGGCTAT 60.804 45.833 0.00 0.00 39.01 2.97
47 48 5.568825 GCCGATCTTTATCCACAAGGCTATA 60.569 44.000 0.00 0.00 39.01 1.31
48 49 6.644347 CCGATCTTTATCCACAAGGCTATAT 58.356 40.000 0.00 0.00 33.74 0.86
49 50 7.106239 CCGATCTTTATCCACAAGGCTATATT 58.894 38.462 0.00 0.00 33.74 1.28
50 51 7.607991 CCGATCTTTATCCACAAGGCTATATTT 59.392 37.037 0.00 0.00 33.74 1.40
51 52 9.003658 CGATCTTTATCCACAAGGCTATATTTT 57.996 33.333 0.00 0.00 33.74 1.82
75 76 8.980481 TTTTTGTTTCTCTCATTAGTCCTTCT 57.020 30.769 0.00 0.00 0.00 2.85
76 77 8.608844 TTTTGTTTCTCTCATTAGTCCTTCTC 57.391 34.615 0.00 0.00 0.00 2.87
77 78 6.918067 TGTTTCTCTCATTAGTCCTTCTCA 57.082 37.500 0.00 0.00 0.00 3.27
78 79 7.487822 TGTTTCTCTCATTAGTCCTTCTCAT 57.512 36.000 0.00 0.00 0.00 2.90
79 80 7.551585 TGTTTCTCTCATTAGTCCTTCTCATC 58.448 38.462 0.00 0.00 0.00 2.92
80 81 6.723298 TTCTCTCATTAGTCCTTCTCATCC 57.277 41.667 0.00 0.00 0.00 3.51
81 82 6.024563 TCTCTCATTAGTCCTTCTCATCCT 57.975 41.667 0.00 0.00 0.00 3.24
82 83 7.155442 TCTCTCATTAGTCCTTCTCATCCTA 57.845 40.000 0.00 0.00 0.00 2.94
83 84 7.764617 TCTCTCATTAGTCCTTCTCATCCTAT 58.235 38.462 0.00 0.00 0.00 2.57
84 85 7.888021 TCTCTCATTAGTCCTTCTCATCCTATC 59.112 40.741 0.00 0.00 0.00 2.08
85 86 7.764617 TCTCATTAGTCCTTCTCATCCTATCT 58.235 38.462 0.00 0.00 0.00 1.98
86 87 7.888021 TCTCATTAGTCCTTCTCATCCTATCTC 59.112 40.741 0.00 0.00 0.00 2.75
87 88 7.764617 TCATTAGTCCTTCTCATCCTATCTCT 58.235 38.462 0.00 0.00 0.00 3.10
88 89 7.888021 TCATTAGTCCTTCTCATCCTATCTCTC 59.112 40.741 0.00 0.00 0.00 3.20
89 90 5.661503 AGTCCTTCTCATCCTATCTCTCA 57.338 43.478 0.00 0.00 0.00 3.27
90 91 6.218195 AGTCCTTCTCATCCTATCTCTCAT 57.782 41.667 0.00 0.00 0.00 2.90
91 92 6.623329 AGTCCTTCTCATCCTATCTCTCATT 58.377 40.000 0.00 0.00 0.00 2.57
92 93 7.075148 AGTCCTTCTCATCCTATCTCTCATTT 58.925 38.462 0.00 0.00 0.00 2.32
93 94 7.568366 AGTCCTTCTCATCCTATCTCTCATTTT 59.432 37.037 0.00 0.00 0.00 1.82
94 95 8.865090 GTCCTTCTCATCCTATCTCTCATTTTA 58.135 37.037 0.00 0.00 0.00 1.52
95 96 8.865090 TCCTTCTCATCCTATCTCTCATTTTAC 58.135 37.037 0.00 0.00 0.00 2.01
96 97 7.812191 CCTTCTCATCCTATCTCTCATTTTACG 59.188 40.741 0.00 0.00 0.00 3.18
97 98 7.825331 TCTCATCCTATCTCTCATTTTACGT 57.175 36.000 0.00 0.00 0.00 3.57
98 99 7.652727 TCTCATCCTATCTCTCATTTTACGTG 58.347 38.462 0.00 0.00 0.00 4.49
99 100 6.216569 TCATCCTATCTCTCATTTTACGTGC 58.783 40.000 0.00 0.00 0.00 5.34
100 101 4.607955 TCCTATCTCTCATTTTACGTGCG 58.392 43.478 0.00 0.00 0.00 5.34
101 102 3.182572 CCTATCTCTCATTTTACGTGCGC 59.817 47.826 0.00 0.00 0.00 6.09
102 103 0.989164 TCTCTCATTTTACGTGCGCG 59.011 50.000 19.78 19.78 44.93 6.86
103 104 0.989164 CTCTCATTTTACGTGCGCGA 59.011 50.000 28.73 7.22 42.00 5.87
104 105 1.388768 CTCTCATTTTACGTGCGCGAA 59.611 47.619 28.73 10.99 42.00 4.70
105 106 1.125384 TCTCATTTTACGTGCGCGAAC 59.875 47.619 28.73 9.55 42.00 3.95
106 107 0.859882 TCATTTTACGTGCGCGAACA 59.140 45.000 28.73 9.70 42.00 3.18
107 108 1.461512 TCATTTTACGTGCGCGAACAT 59.538 42.857 28.73 3.91 42.00 2.71
108 109 2.096169 TCATTTTACGTGCGCGAACATT 60.096 40.909 28.73 5.74 42.00 2.71
109 110 2.386501 TTTTACGTGCGCGAACATTT 57.613 40.000 28.73 4.87 42.00 2.32
110 111 2.386501 TTTACGTGCGCGAACATTTT 57.613 40.000 28.73 4.03 42.00 1.82
111 112 2.386501 TTACGTGCGCGAACATTTTT 57.613 40.000 28.73 3.18 42.00 1.94
132 133 5.896922 TTTTTCATGTGCGTGGTTATTTG 57.103 34.783 0.00 0.00 0.00 2.32
133 134 3.567576 TTCATGTGCGTGGTTATTTGG 57.432 42.857 0.00 0.00 0.00 3.28
134 135 2.509569 TCATGTGCGTGGTTATTTGGT 58.490 42.857 0.00 0.00 0.00 3.67
135 136 2.887783 TCATGTGCGTGGTTATTTGGTT 59.112 40.909 0.00 0.00 0.00 3.67
136 137 3.319405 TCATGTGCGTGGTTATTTGGTTT 59.681 39.130 0.00 0.00 0.00 3.27
137 138 3.357166 TGTGCGTGGTTATTTGGTTTC 57.643 42.857 0.00 0.00 0.00 2.78
138 139 2.952978 TGTGCGTGGTTATTTGGTTTCT 59.047 40.909 0.00 0.00 0.00 2.52
139 140 3.243234 TGTGCGTGGTTATTTGGTTTCTG 60.243 43.478 0.00 0.00 0.00 3.02
140 141 2.952978 TGCGTGGTTATTTGGTTTCTGT 59.047 40.909 0.00 0.00 0.00 3.41
141 142 3.381908 TGCGTGGTTATTTGGTTTCTGTT 59.618 39.130 0.00 0.00 0.00 3.16
142 143 4.142138 TGCGTGGTTATTTGGTTTCTGTTT 60.142 37.500 0.00 0.00 0.00 2.83
143 144 4.806775 GCGTGGTTATTTGGTTTCTGTTTT 59.193 37.500 0.00 0.00 0.00 2.43
144 145 5.051307 GCGTGGTTATTTGGTTTCTGTTTTC 60.051 40.000 0.00 0.00 0.00 2.29
145 146 6.270064 CGTGGTTATTTGGTTTCTGTTTTCT 58.730 36.000 0.00 0.00 0.00 2.52
146 147 6.198216 CGTGGTTATTTGGTTTCTGTTTTCTG 59.802 38.462 0.00 0.00 0.00 3.02
147 148 7.039270 GTGGTTATTTGGTTTCTGTTTTCTGT 58.961 34.615 0.00 0.00 0.00 3.41
148 149 7.547722 GTGGTTATTTGGTTTCTGTTTTCTGTT 59.452 33.333 0.00 0.00 0.00 3.16
149 150 8.097662 TGGTTATTTGGTTTCTGTTTTCTGTTT 58.902 29.630 0.00 0.00 0.00 2.83
150 151 8.600625 GGTTATTTGGTTTCTGTTTTCTGTTTC 58.399 33.333 0.00 0.00 0.00 2.78
151 152 6.885735 ATTTGGTTTCTGTTTTCTGTTTCG 57.114 33.333 0.00 0.00 0.00 3.46
152 153 5.379732 TTGGTTTCTGTTTTCTGTTTCGT 57.620 34.783 0.00 0.00 0.00 3.85
153 154 4.728534 TGGTTTCTGTTTTCTGTTTCGTG 58.271 39.130 0.00 0.00 0.00 4.35
154 155 4.216687 TGGTTTCTGTTTTCTGTTTCGTGT 59.783 37.500 0.00 0.00 0.00 4.49
155 156 5.158494 GGTTTCTGTTTTCTGTTTCGTGTT 58.842 37.500 0.00 0.00 0.00 3.32
156 157 5.631929 GGTTTCTGTTTTCTGTTTCGTGTTT 59.368 36.000 0.00 0.00 0.00 2.83
157 158 6.144886 GGTTTCTGTTTTCTGTTTCGTGTTTT 59.855 34.615 0.00 0.00 0.00 2.43
158 159 7.306925 GGTTTCTGTTTTCTGTTTCGTGTTTTT 60.307 33.333 0.00 0.00 0.00 1.94
205 206 8.667076 AGTTTTCCTTTCATTTTCCAGATTTG 57.333 30.769 0.00 0.00 0.00 2.32
206 207 7.716560 AGTTTTCCTTTCATTTTCCAGATTTGG 59.283 33.333 0.00 0.00 46.49 3.28
207 208 6.745794 TTCCTTTCATTTTCCAGATTTGGT 57.254 33.333 1.59 0.00 45.26 3.67
208 209 6.745794 TCCTTTCATTTTCCAGATTTGGTT 57.254 33.333 1.59 0.00 45.26 3.67
209 210 7.135591 TCCTTTCATTTTCCAGATTTGGTTT 57.864 32.000 1.59 0.00 45.26 3.27
210 211 7.572814 TCCTTTCATTTTCCAGATTTGGTTTT 58.427 30.769 1.59 0.00 45.26 2.43
211 212 8.052141 TCCTTTCATTTTCCAGATTTGGTTTTT 58.948 29.630 1.59 0.00 45.26 1.94
212 213 8.344831 CCTTTCATTTTCCAGATTTGGTTTTTC 58.655 33.333 1.59 0.00 45.26 2.29
213 214 9.112725 CTTTCATTTTCCAGATTTGGTTTTTCT 57.887 29.630 1.59 0.00 45.26 2.52
214 215 9.460019 TTTCATTTTCCAGATTTGGTTTTTCTT 57.540 25.926 1.59 0.00 45.26 2.52
215 216 8.661352 TCATTTTCCAGATTTGGTTTTTCTTC 57.339 30.769 1.59 0.00 45.26 2.87
216 217 8.485392 TCATTTTCCAGATTTGGTTTTTCTTCT 58.515 29.630 1.59 0.00 45.26 2.85
217 218 8.553696 CATTTTCCAGATTTGGTTTTTCTTCTG 58.446 33.333 1.59 0.00 45.26 3.02
218 219 7.416964 TTTCCAGATTTGGTTTTTCTTCTGA 57.583 32.000 1.59 0.00 45.26 3.27
219 220 7.416964 TTCCAGATTTGGTTTTTCTTCTGAA 57.583 32.000 1.59 0.00 45.26 3.02
220 221 7.601705 TCCAGATTTGGTTTTTCTTCTGAAT 57.398 32.000 1.59 0.00 45.26 2.57
221 222 8.021898 TCCAGATTTGGTTTTTCTTCTGAATT 57.978 30.769 1.59 0.00 45.26 2.17
222 223 8.485392 TCCAGATTTGGTTTTTCTTCTGAATTT 58.515 29.630 1.59 0.00 45.26 1.82
223 224 9.112725 CCAGATTTGGTTTTTCTTCTGAATTTT 57.887 29.630 0.00 0.00 39.79 1.82
287 288 7.767261 TGGTTAACATTTATCAAGTACATGCC 58.233 34.615 8.10 0.00 0.00 4.40
288 289 6.910433 GGTTAACATTTATCAAGTACATGCCG 59.090 38.462 8.10 0.00 0.00 5.69
289 290 7.201661 GGTTAACATTTATCAAGTACATGCCGA 60.202 37.037 8.10 0.00 0.00 5.54
290 291 6.751514 AACATTTATCAAGTACATGCCGAA 57.248 33.333 0.00 0.00 0.00 4.30
291 292 6.119144 ACATTTATCAAGTACATGCCGAAC 57.881 37.500 0.00 0.00 0.00 3.95
292 293 5.880332 ACATTTATCAAGTACATGCCGAACT 59.120 36.000 0.00 0.00 0.00 3.01
293 294 6.374333 ACATTTATCAAGTACATGCCGAACTT 59.626 34.615 0.00 0.00 33.82 2.66
294 295 6.811253 TTTATCAAGTACATGCCGAACTTT 57.189 33.333 0.00 0.00 31.21 2.66
295 296 6.811253 TTATCAAGTACATGCCGAACTTTT 57.189 33.333 0.00 0.00 31.21 2.27
296 297 5.705609 ATCAAGTACATGCCGAACTTTTT 57.294 34.783 0.00 0.00 31.21 1.94
509 510 8.953368 TTTTTCTAAAATATACTCCCTCCGTC 57.047 34.615 0.00 0.00 0.00 4.79
510 511 6.661304 TTCTAAAATATACTCCCTCCGTCC 57.339 41.667 0.00 0.00 0.00 4.79
511 512 5.082425 TCTAAAATATACTCCCTCCGTCCC 58.918 45.833 0.00 0.00 0.00 4.46
512 513 3.339713 AAATATACTCCCTCCGTCCCA 57.660 47.619 0.00 0.00 0.00 4.37
513 514 3.562108 AATATACTCCCTCCGTCCCAT 57.438 47.619 0.00 0.00 0.00 4.00
514 515 4.687262 AATATACTCCCTCCGTCCCATA 57.313 45.455 0.00 0.00 0.00 2.74
515 516 4.687262 ATATACTCCCTCCGTCCCATAA 57.313 45.455 0.00 0.00 0.00 1.90
516 517 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
517 518 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
518 519 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
519 520 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
520 521 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
521 522 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
522 523 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
523 524 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
524 525 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
525 526 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
526 527 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
527 528 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
528 529 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
529 530 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
530 531 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
531 532 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
532 533 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
533 534 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
534 535 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
535 536 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
536 537 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
539 540 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
540 541 4.531659 AAGAGCGTTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
541 542 3.527533 AGAGCGTTTTTGACACTACACA 58.472 40.909 0.00 0.00 0.00 3.72
542 543 3.936453 AGAGCGTTTTTGACACTACACAA 59.064 39.130 0.00 0.00 0.00 3.33
543 544 4.034048 AGAGCGTTTTTGACACTACACAAG 59.966 41.667 0.00 0.00 0.00 3.16
544 545 3.687698 AGCGTTTTTGACACTACACAAGT 59.312 39.130 0.00 0.00 39.81 3.16
555 556 4.011058 ACTACACAAGTGTCAAAAACGC 57.989 40.909 9.42 0.00 43.74 4.84
560 561 3.074594 AGTGTCAAAAACGCTCCGT 57.925 47.368 0.00 0.00 45.69 4.69
561 562 0.935196 AGTGTCAAAAACGCTCCGTC 59.065 50.000 0.00 0.00 45.69 4.79
562 563 0.041576 GTGTCAAAAACGCTCCGTCC 60.042 55.000 0.00 0.00 39.99 4.79
563 564 1.161563 TGTCAAAAACGCTCCGTCCC 61.162 55.000 0.00 0.00 39.99 4.46
564 565 1.146485 TCAAAAACGCTCCGTCCCA 59.854 52.632 0.00 0.00 39.99 4.37
565 566 0.250553 TCAAAAACGCTCCGTCCCAT 60.251 50.000 0.00 0.00 39.99 4.00
566 567 1.002201 TCAAAAACGCTCCGTCCCATA 59.998 47.619 0.00 0.00 39.99 2.74
567 568 1.807742 CAAAAACGCTCCGTCCCATAA 59.192 47.619 0.00 0.00 39.99 1.90
568 569 2.413310 AAAACGCTCCGTCCCATAAT 57.587 45.000 0.00 0.00 39.99 1.28
569 570 3.547054 AAAACGCTCCGTCCCATAATA 57.453 42.857 0.00 0.00 39.99 0.98
570 571 3.764237 AAACGCTCCGTCCCATAATAT 57.236 42.857 0.00 0.00 39.99 1.28
571 572 4.877378 AAACGCTCCGTCCCATAATATA 57.123 40.909 0.00 0.00 39.99 0.86
572 573 4.877378 AACGCTCCGTCCCATAATATAA 57.123 40.909 0.00 0.00 39.99 0.98
573 574 4.451629 ACGCTCCGTCCCATAATATAAG 57.548 45.455 0.00 0.00 33.69 1.73
574 575 4.084287 ACGCTCCGTCCCATAATATAAGA 58.916 43.478 0.00 0.00 33.69 2.10
575 576 4.158025 ACGCTCCGTCCCATAATATAAGAG 59.842 45.833 0.00 0.00 33.69 2.85
576 577 4.434520 GCTCCGTCCCATAATATAAGAGC 58.565 47.826 0.00 0.00 37.64 4.09
577 578 4.673441 CTCCGTCCCATAATATAAGAGCG 58.327 47.826 0.00 0.00 0.00 5.03
578 579 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
579 580 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
580 581 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
581 582 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
582 583 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
583 584 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
584 585 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
585 586 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
586 587 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
587 588 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
588 589 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
591 592 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
592 593 4.531659 AAGAGCGTTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
593 594 3.527533 AGAGCGTTTTTGACACTACACA 58.472 40.909 0.00 0.00 0.00 3.72
594 595 3.936453 AGAGCGTTTTTGACACTACACAA 59.064 39.130 0.00 0.00 0.00 3.33
595 596 4.034048 AGAGCGTTTTTGACACTACACAAG 59.966 41.667 0.00 0.00 0.00 3.16
596 597 3.687698 AGCGTTTTTGACACTACACAAGT 59.312 39.130 0.00 0.00 39.81 3.16
597 598 4.871557 AGCGTTTTTGACACTACACAAGTA 59.128 37.500 0.00 0.00 35.76 2.24
598 599 5.526111 AGCGTTTTTGACACTACACAAGTAT 59.474 36.000 0.00 0.00 35.76 2.12
599 600 6.702723 AGCGTTTTTGACACTACACAAGTATA 59.297 34.615 0.00 0.00 35.76 1.47
600 601 7.386848 AGCGTTTTTGACACTACACAAGTATAT 59.613 33.333 0.00 0.00 35.76 0.86
601 602 8.013378 GCGTTTTTGACACTACACAAGTATATT 58.987 33.333 0.00 0.00 35.76 1.28
602 603 9.872757 CGTTTTTGACACTACACAAGTATATTT 57.127 29.630 0.00 0.00 35.76 1.40
675 676 3.259314 TCATGGGCAGTGTGGGCT 61.259 61.111 0.00 0.00 0.00 5.19
692 693 1.434696 CTGTCCCATTTGCGATGGC 59.565 57.895 12.25 0.00 37.85 4.40
696 697 1.142314 CCCATTTGCGATGGCCTTG 59.858 57.895 3.32 0.00 37.85 3.61
703 704 2.817423 GCGATGGCCTTGAGCGAAG 61.817 63.158 3.32 0.00 45.17 3.79
721 722 0.533032 AGGCTCTCCTTCTGTAACGC 59.467 55.000 0.00 0.00 40.66 4.84
722 723 0.246635 GGCTCTCCTTCTGTAACGCA 59.753 55.000 0.00 0.00 0.00 5.24
723 724 1.351153 GCTCTCCTTCTGTAACGCAC 58.649 55.000 0.00 0.00 0.00 5.34
724 725 1.067495 GCTCTCCTTCTGTAACGCACT 60.067 52.381 0.00 0.00 0.00 4.40
726 727 2.229062 CTCTCCTTCTGTAACGCACTGA 59.771 50.000 0.00 0.00 33.68 3.41
727 728 2.229062 TCTCCTTCTGTAACGCACTGAG 59.771 50.000 0.00 0.00 36.58 3.35
728 729 1.071605 CCTTCTGTAACGCACTGAGC 58.928 55.000 0.00 0.00 36.58 4.26
729 730 1.337260 CCTTCTGTAACGCACTGAGCT 60.337 52.381 0.00 0.00 42.61 4.09
730 731 1.723542 CTTCTGTAACGCACTGAGCTG 59.276 52.381 0.00 0.00 42.61 4.24
731 732 0.958822 TCTGTAACGCACTGAGCTGA 59.041 50.000 0.00 0.00 42.61 4.26
732 733 1.339929 TCTGTAACGCACTGAGCTGAA 59.660 47.619 0.00 0.00 42.61 3.02
733 734 2.135139 CTGTAACGCACTGAGCTGAAA 58.865 47.619 0.00 0.00 42.61 2.69
734 735 1.864711 TGTAACGCACTGAGCTGAAAC 59.135 47.619 0.00 0.00 42.61 2.78
735 736 1.864711 GTAACGCACTGAGCTGAAACA 59.135 47.619 0.00 0.00 42.61 2.83
736 737 1.597742 AACGCACTGAGCTGAAACAT 58.402 45.000 0.00 0.00 42.61 2.71
737 738 2.455674 ACGCACTGAGCTGAAACATA 57.544 45.000 0.00 0.00 42.61 2.29
742 743 6.459066 ACGCACTGAGCTGAAACATATATAT 58.541 36.000 0.00 0.00 42.61 0.86
751 752 6.149474 AGCTGAAACATATATATTCCGGTTGC 59.851 38.462 0.00 0.00 0.00 4.17
785 786 3.666253 CGTCGCCAAAACCCCACC 61.666 66.667 0.00 0.00 0.00 4.61
791 792 0.464735 GCCAAAACCCCACCCAAAAC 60.465 55.000 0.00 0.00 0.00 2.43
798 799 4.614036 CCACCCAAAACCCCGCCT 62.614 66.667 0.00 0.00 0.00 5.52
817 818 2.203750 TGGCATGCCCAAAAGGGT 59.796 55.556 33.44 0.00 41.82 4.34
820 821 0.249120 GGCATGCCCAAAAGGGTTAC 59.751 55.000 27.24 0.00 35.41 2.50
821 822 0.972883 GCATGCCCAAAAGGGTTACA 59.027 50.000 6.36 0.00 35.41 2.41
892 901 1.525077 CCTCGGTCTCTCTCCTCCG 60.525 68.421 0.00 0.00 43.65 4.63
1372 1417 1.658931 CGTTCGACGAAATGCTTGCAA 60.659 47.619 12.67 0.00 46.05 4.08
1456 1504 2.090524 CGGTTTGACCTCGCGTACC 61.091 63.158 5.77 2.98 35.66 3.34
1473 1521 1.874129 ACCAGGTGATCATCCGGTTA 58.126 50.000 8.15 0.00 31.61 2.85
1549 1597 3.311110 GCCGTGTGGGGAGAGTGA 61.311 66.667 0.00 0.00 35.78 3.41
1626 1674 2.660490 CAAACTTACACGCCCATTGTG 58.340 47.619 0.00 0.00 42.99 3.33
1951 2002 8.862325 TTTGAGTATTCTTCTGAATTGCCTTA 57.138 30.769 0.00 0.00 42.37 2.69
1997 2048 1.134699 CGTATGCTTGCTGGAGAGGAA 60.135 52.381 0.00 0.00 0.00 3.36
2315 2369 6.418101 ACCTAATATTTGACATGACAGCAGT 58.582 36.000 0.00 0.00 0.00 4.40
2637 2697 4.054780 TGTTCTAGATACGATGTTGGGC 57.945 45.455 0.00 0.00 0.00 5.36
2676 2736 3.132289 CCTTGTGTATCTAGGAAAGCCGA 59.868 47.826 0.00 0.00 40.60 5.54
3151 3215 2.031682 CGTTTTTCTGCCTGGTTCTCAG 60.032 50.000 0.00 0.00 43.00 3.35
3177 3241 3.004106 GGGATGCAAATTTCTGATCCTCG 59.996 47.826 14.84 0.00 34.20 4.63
3215 3279 5.288804 CCTCGTTTGTTCAACCAAATGAAT 58.711 37.500 9.16 0.00 45.06 2.57
3599 5870 2.810400 GCACAAAGTAGCACTCCCTCAA 60.810 50.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.345760 CCCATGTTGGCTGAGCACC 61.346 63.158 6.82 0.00 35.79 5.01
1 2 1.181098 AACCCATGTTGGCTGAGCAC 61.181 55.000 6.82 0.00 35.79 4.40
2 3 0.469705 AAACCCATGTTGGCTGAGCA 60.470 50.000 6.82 0.00 35.79 4.26
3 4 0.037975 CAAACCCATGTTGGCTGAGC 60.038 55.000 0.00 0.00 35.79 4.26
4 5 0.604578 CCAAACCCATGTTGGCTGAG 59.395 55.000 0.99 0.00 35.79 3.35
5 6 1.470996 GCCAAACCCATGTTGGCTGA 61.471 55.000 24.22 0.00 41.47 4.26
6 7 1.004679 GCCAAACCCATGTTGGCTG 60.005 57.895 24.22 7.29 41.47 4.85
7 8 2.216331 GGCCAAACCCATGTTGGCT 61.216 57.895 27.96 0.00 42.90 4.75
8 9 2.347114 GGCCAAACCCATGTTGGC 59.653 61.111 23.72 23.72 42.74 4.52
9 10 1.257055 ATCGGCCAAACCCATGTTGG 61.257 55.000 2.24 8.81 37.25 3.77
10 11 0.173255 GATCGGCCAAACCCATGTTG 59.827 55.000 2.24 0.00 34.13 3.33
11 12 0.039618 AGATCGGCCAAACCCATGTT 59.960 50.000 2.24 0.00 35.82 2.71
12 13 0.039618 AAGATCGGCCAAACCCATGT 59.960 50.000 2.24 0.00 33.26 3.21
13 14 1.185315 AAAGATCGGCCAAACCCATG 58.815 50.000 2.24 0.00 33.26 3.66
14 15 2.818751 TAAAGATCGGCCAAACCCAT 57.181 45.000 2.24 0.00 33.26 4.00
15 16 2.650322 GATAAAGATCGGCCAAACCCA 58.350 47.619 2.24 0.00 33.26 4.51
16 17 1.954382 GGATAAAGATCGGCCAAACCC 59.046 52.381 2.24 0.00 32.28 4.11
17 18 2.357952 GTGGATAAAGATCGGCCAAACC 59.642 50.000 2.24 0.00 32.28 3.27
18 19 3.013921 TGTGGATAAAGATCGGCCAAAC 58.986 45.455 2.24 0.00 32.28 2.93
19 20 3.358111 TGTGGATAAAGATCGGCCAAA 57.642 42.857 2.24 0.00 32.28 3.28
20 21 3.278574 CTTGTGGATAAAGATCGGCCAA 58.721 45.455 2.24 0.00 32.28 4.52
21 22 2.421388 CCTTGTGGATAAAGATCGGCCA 60.421 50.000 2.24 0.00 34.57 5.36
22 23 2.222027 CCTTGTGGATAAAGATCGGCC 58.778 52.381 0.00 0.00 34.57 6.13
23 24 1.604278 GCCTTGTGGATAAAGATCGGC 59.396 52.381 0.00 0.00 34.57 5.54
24 25 3.199880 AGCCTTGTGGATAAAGATCGG 57.800 47.619 0.00 0.00 34.57 4.18
25 26 8.553459 AAATATAGCCTTGTGGATAAAGATCG 57.447 34.615 0.00 0.00 37.79 3.69
50 51 8.980481 AGAAGGACTAATGAGAGAAACAAAAA 57.020 30.769 0.00 0.00 0.00 1.94
51 52 8.210946 TGAGAAGGACTAATGAGAGAAACAAAA 58.789 33.333 0.00 0.00 0.00 2.44
52 53 7.735917 TGAGAAGGACTAATGAGAGAAACAAA 58.264 34.615 0.00 0.00 0.00 2.83
53 54 7.303182 TGAGAAGGACTAATGAGAGAAACAA 57.697 36.000 0.00 0.00 0.00 2.83
54 55 6.918067 TGAGAAGGACTAATGAGAGAAACA 57.082 37.500 0.00 0.00 0.00 2.83
55 56 6.983890 GGATGAGAAGGACTAATGAGAGAAAC 59.016 42.308 0.00 0.00 0.00 2.78
56 57 6.900186 AGGATGAGAAGGACTAATGAGAGAAA 59.100 38.462 0.00 0.00 0.00 2.52
57 58 6.439487 AGGATGAGAAGGACTAATGAGAGAA 58.561 40.000 0.00 0.00 0.00 2.87
58 59 6.024563 AGGATGAGAAGGACTAATGAGAGA 57.975 41.667 0.00 0.00 0.00 3.10
59 60 7.890127 AGATAGGATGAGAAGGACTAATGAGAG 59.110 40.741 0.00 0.00 0.00 3.20
60 61 7.764617 AGATAGGATGAGAAGGACTAATGAGA 58.235 38.462 0.00 0.00 0.00 3.27
61 62 7.890127 AGAGATAGGATGAGAAGGACTAATGAG 59.110 40.741 0.00 0.00 0.00 2.90
62 63 7.764617 AGAGATAGGATGAGAAGGACTAATGA 58.235 38.462 0.00 0.00 0.00 2.57
63 64 7.669304 TGAGAGATAGGATGAGAAGGACTAATG 59.331 40.741 0.00 0.00 0.00 1.90
64 65 7.764617 TGAGAGATAGGATGAGAAGGACTAAT 58.235 38.462 0.00 0.00 0.00 1.73
65 66 7.155442 TGAGAGATAGGATGAGAAGGACTAA 57.845 40.000 0.00 0.00 0.00 2.24
66 67 6.771934 TGAGAGATAGGATGAGAAGGACTA 57.228 41.667 0.00 0.00 0.00 2.59
67 68 5.661503 TGAGAGATAGGATGAGAAGGACT 57.338 43.478 0.00 0.00 0.00 3.85
68 69 6.916360 AATGAGAGATAGGATGAGAAGGAC 57.084 41.667 0.00 0.00 0.00 3.85
69 70 7.927683 AAAATGAGAGATAGGATGAGAAGGA 57.072 36.000 0.00 0.00 0.00 3.36
70 71 7.812191 CGTAAAATGAGAGATAGGATGAGAAGG 59.188 40.741 0.00 0.00 0.00 3.46
71 72 8.356657 ACGTAAAATGAGAGATAGGATGAGAAG 58.643 37.037 0.00 0.00 0.00 2.85
72 73 8.138074 CACGTAAAATGAGAGATAGGATGAGAA 58.862 37.037 0.00 0.00 0.00 2.87
73 74 7.652727 CACGTAAAATGAGAGATAGGATGAGA 58.347 38.462 0.00 0.00 0.00 3.27
74 75 6.364706 GCACGTAAAATGAGAGATAGGATGAG 59.635 42.308 0.00 0.00 0.00 2.90
75 76 6.216569 GCACGTAAAATGAGAGATAGGATGA 58.783 40.000 0.00 0.00 0.00 2.92
76 77 5.117745 CGCACGTAAAATGAGAGATAGGATG 59.882 44.000 0.00 0.00 0.00 3.51
77 78 5.223382 CGCACGTAAAATGAGAGATAGGAT 58.777 41.667 0.00 0.00 0.00 3.24
78 79 4.607955 CGCACGTAAAATGAGAGATAGGA 58.392 43.478 0.00 0.00 0.00 2.94
79 80 3.182572 GCGCACGTAAAATGAGAGATAGG 59.817 47.826 0.30 0.00 0.00 2.57
80 81 3.121663 CGCGCACGTAAAATGAGAGATAG 60.122 47.826 8.75 0.00 33.53 2.08
81 82 2.787129 CGCGCACGTAAAATGAGAGATA 59.213 45.455 8.75 0.00 33.53 1.98
82 83 1.588404 CGCGCACGTAAAATGAGAGAT 59.412 47.619 8.75 0.00 33.53 2.75
83 84 0.989164 CGCGCACGTAAAATGAGAGA 59.011 50.000 8.75 0.00 33.53 3.10
84 85 0.989164 TCGCGCACGTAAAATGAGAG 59.011 50.000 8.75 0.00 41.18 3.20
85 86 1.125384 GTTCGCGCACGTAAAATGAGA 59.875 47.619 8.75 0.00 41.18 3.27
86 87 1.136474 TGTTCGCGCACGTAAAATGAG 60.136 47.619 8.75 0.00 41.18 2.90
87 88 0.859882 TGTTCGCGCACGTAAAATGA 59.140 45.000 8.75 0.00 41.18 2.57
88 89 1.877101 ATGTTCGCGCACGTAAAATG 58.123 45.000 8.75 0.00 41.18 2.32
89 90 2.604969 AATGTTCGCGCACGTAAAAT 57.395 40.000 8.75 0.00 41.18 1.82
90 91 2.386501 AAATGTTCGCGCACGTAAAA 57.613 40.000 8.75 0.00 41.18 1.52
91 92 2.386501 AAAATGTTCGCGCACGTAAA 57.613 40.000 8.75 0.00 41.18 2.01
92 93 2.386501 AAAAATGTTCGCGCACGTAA 57.613 40.000 8.75 0.00 41.18 3.18
110 111 4.747108 CCAAATAACCACGCACATGAAAAA 59.253 37.500 0.00 0.00 0.00 1.94
111 112 4.202161 ACCAAATAACCACGCACATGAAAA 60.202 37.500 0.00 0.00 0.00 2.29
112 113 3.319405 ACCAAATAACCACGCACATGAAA 59.681 39.130 0.00 0.00 0.00 2.69
113 114 2.887783 ACCAAATAACCACGCACATGAA 59.112 40.909 0.00 0.00 0.00 2.57
114 115 2.509569 ACCAAATAACCACGCACATGA 58.490 42.857 0.00 0.00 0.00 3.07
115 116 3.296322 AACCAAATAACCACGCACATG 57.704 42.857 0.00 0.00 0.00 3.21
116 117 3.572255 AGAAACCAAATAACCACGCACAT 59.428 39.130 0.00 0.00 0.00 3.21
117 118 2.952978 AGAAACCAAATAACCACGCACA 59.047 40.909 0.00 0.00 0.00 4.57
118 119 3.243267 ACAGAAACCAAATAACCACGCAC 60.243 43.478 0.00 0.00 0.00 5.34
119 120 2.952978 ACAGAAACCAAATAACCACGCA 59.047 40.909 0.00 0.00 0.00 5.24
120 121 3.636282 ACAGAAACCAAATAACCACGC 57.364 42.857 0.00 0.00 0.00 5.34
121 122 6.198216 CAGAAAACAGAAACCAAATAACCACG 59.802 38.462 0.00 0.00 0.00 4.94
122 123 7.039270 ACAGAAAACAGAAACCAAATAACCAC 58.961 34.615 0.00 0.00 0.00 4.16
123 124 7.176589 ACAGAAAACAGAAACCAAATAACCA 57.823 32.000 0.00 0.00 0.00 3.67
124 125 8.487313 AAACAGAAAACAGAAACCAAATAACC 57.513 30.769 0.00 0.00 0.00 2.85
125 126 8.318167 CGAAACAGAAAACAGAAACCAAATAAC 58.682 33.333 0.00 0.00 0.00 1.89
126 127 8.030106 ACGAAACAGAAAACAGAAACCAAATAA 58.970 29.630 0.00 0.00 0.00 1.40
127 128 7.486551 CACGAAACAGAAAACAGAAACCAAATA 59.513 33.333 0.00 0.00 0.00 1.40
128 129 6.310224 CACGAAACAGAAAACAGAAACCAAAT 59.690 34.615 0.00 0.00 0.00 2.32
129 130 5.631512 CACGAAACAGAAAACAGAAACCAAA 59.368 36.000 0.00 0.00 0.00 3.28
130 131 5.157781 CACGAAACAGAAAACAGAAACCAA 58.842 37.500 0.00 0.00 0.00 3.67
131 132 4.216687 ACACGAAACAGAAAACAGAAACCA 59.783 37.500 0.00 0.00 0.00 3.67
132 133 4.729595 ACACGAAACAGAAAACAGAAACC 58.270 39.130 0.00 0.00 0.00 3.27
133 134 6.684609 AAACACGAAACAGAAAACAGAAAC 57.315 33.333 0.00 0.00 0.00 2.78
134 135 7.701809 AAAAACACGAAACAGAAAACAGAAA 57.298 28.000 0.00 0.00 0.00 2.52
179 180 9.762933 CAAATCTGGAAAATGAAAGGAAAACTA 57.237 29.630 0.00 0.00 0.00 2.24
180 181 7.716560 CCAAATCTGGAAAATGAAAGGAAAACT 59.283 33.333 0.00 0.00 46.92 2.66
181 182 7.498900 ACCAAATCTGGAAAATGAAAGGAAAAC 59.501 33.333 0.00 0.00 46.92 2.43
182 183 7.572814 ACCAAATCTGGAAAATGAAAGGAAAA 58.427 30.769 0.00 0.00 46.92 2.29
183 184 7.135591 ACCAAATCTGGAAAATGAAAGGAAA 57.864 32.000 0.00 0.00 46.92 3.13
184 185 6.745794 ACCAAATCTGGAAAATGAAAGGAA 57.254 33.333 0.00 0.00 46.92 3.36
185 186 6.745794 AACCAAATCTGGAAAATGAAAGGA 57.254 33.333 0.00 0.00 46.92 3.36
186 187 7.806409 AAAACCAAATCTGGAAAATGAAAGG 57.194 32.000 0.00 0.00 46.92 3.11
187 188 9.112725 AGAAAAACCAAATCTGGAAAATGAAAG 57.887 29.630 0.00 0.00 46.92 2.62
188 189 9.460019 AAGAAAAACCAAATCTGGAAAATGAAA 57.540 25.926 0.00 0.00 46.92 2.69
189 190 9.108284 GAAGAAAAACCAAATCTGGAAAATGAA 57.892 29.630 0.00 0.00 46.92 2.57
190 191 8.485392 AGAAGAAAAACCAAATCTGGAAAATGA 58.515 29.630 0.00 0.00 46.92 2.57
191 192 8.553696 CAGAAGAAAAACCAAATCTGGAAAATG 58.446 33.333 0.00 0.00 46.92 2.32
192 193 8.485392 TCAGAAGAAAAACCAAATCTGGAAAAT 58.515 29.630 0.00 0.00 46.92 1.82
193 194 7.846066 TCAGAAGAAAAACCAAATCTGGAAAA 58.154 30.769 0.00 0.00 46.92 2.29
194 195 7.416964 TCAGAAGAAAAACCAAATCTGGAAA 57.583 32.000 0.00 0.00 46.92 3.13
195 196 7.416964 TTCAGAAGAAAAACCAAATCTGGAA 57.583 32.000 0.00 0.00 46.92 3.53
196 197 7.601705 ATTCAGAAGAAAAACCAAATCTGGA 57.398 32.000 0.00 0.00 40.32 3.86
197 198 8.667076 AAATTCAGAAGAAAAACCAAATCTGG 57.333 30.769 0.00 0.00 42.19 3.86
261 262 8.413229 GGCATGTACTTGATAAATGTTAACCAT 58.587 33.333 12.65 0.00 31.71 3.55
262 263 7.414651 CGGCATGTACTTGATAAATGTTAACCA 60.415 37.037 12.65 0.00 31.71 3.67
263 264 6.910433 CGGCATGTACTTGATAAATGTTAACC 59.090 38.462 12.65 0.00 31.71 2.85
264 265 7.690228 TCGGCATGTACTTGATAAATGTTAAC 58.310 34.615 12.65 0.00 31.71 2.01
265 266 7.851387 TCGGCATGTACTTGATAAATGTTAA 57.149 32.000 12.65 0.00 31.71 2.01
266 267 7.551262 AGTTCGGCATGTACTTGATAAATGTTA 59.449 33.333 12.65 0.00 31.71 2.41
267 268 6.374333 AGTTCGGCATGTACTTGATAAATGTT 59.626 34.615 12.65 0.00 31.71 2.71
268 269 5.880332 AGTTCGGCATGTACTTGATAAATGT 59.120 36.000 12.65 0.00 31.71 2.71
269 270 6.363577 AGTTCGGCATGTACTTGATAAATG 57.636 37.500 12.65 0.00 32.19 2.32
270 271 7.391148 AAAGTTCGGCATGTACTTGATAAAT 57.609 32.000 12.65 0.34 38.11 1.40
271 272 6.811253 AAAGTTCGGCATGTACTTGATAAA 57.189 33.333 12.65 0.56 38.11 1.40
272 273 6.811253 AAAAGTTCGGCATGTACTTGATAA 57.189 33.333 12.65 0.85 38.11 1.75
273 274 6.811253 AAAAAGTTCGGCATGTACTTGATA 57.189 33.333 12.65 0.00 38.11 2.15
274 275 5.705609 AAAAAGTTCGGCATGTACTTGAT 57.294 34.783 12.65 0.00 38.11 2.57
484 485 7.989170 GGACGGAGGGAGTATATTTTAGAAAAA 59.011 37.037 0.00 0.00 0.00 1.94
485 486 7.419403 GGGACGGAGGGAGTATATTTTAGAAAA 60.419 40.741 0.00 0.00 0.00 2.29
486 487 6.042437 GGGACGGAGGGAGTATATTTTAGAAA 59.958 42.308 0.00 0.00 0.00 2.52
487 488 5.541484 GGGACGGAGGGAGTATATTTTAGAA 59.459 44.000 0.00 0.00 0.00 2.10
488 489 5.082425 GGGACGGAGGGAGTATATTTTAGA 58.918 45.833 0.00 0.00 0.00 2.10
489 490 4.836736 TGGGACGGAGGGAGTATATTTTAG 59.163 45.833 0.00 0.00 0.00 1.85
490 491 4.818447 TGGGACGGAGGGAGTATATTTTA 58.182 43.478 0.00 0.00 0.00 1.52
491 492 3.660959 TGGGACGGAGGGAGTATATTTT 58.339 45.455 0.00 0.00 0.00 1.82
492 493 3.339713 TGGGACGGAGGGAGTATATTT 57.660 47.619 0.00 0.00 0.00 1.40
493 494 3.562108 ATGGGACGGAGGGAGTATATT 57.438 47.619 0.00 0.00 0.00 1.28
494 495 4.687262 TTATGGGACGGAGGGAGTATAT 57.313 45.455 0.00 0.00 0.00 0.86
495 496 4.687262 ATTATGGGACGGAGGGAGTATA 57.313 45.455 0.00 0.00 0.00 1.47
496 497 3.562108 ATTATGGGACGGAGGGAGTAT 57.438 47.619 0.00 0.00 0.00 2.12
497 498 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
498 499 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
499 500 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
500 501 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
501 502 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
502 503 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
503 504 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
504 505 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
505 506 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
506 507 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
507 508 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
508 509 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
509 510 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
510 511 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
513 514 9.642327 TGTAGTGTCAAAAACGCTCTTATATTA 57.358 29.630 0.00 0.00 45.69 0.98
514 515 8.440833 GTGTAGTGTCAAAAACGCTCTTATATT 58.559 33.333 0.00 0.00 45.69 1.28
515 516 7.601130 TGTGTAGTGTCAAAAACGCTCTTATAT 59.399 33.333 0.00 0.00 45.69 0.86
516 517 6.924612 TGTGTAGTGTCAAAAACGCTCTTATA 59.075 34.615 0.00 0.00 45.69 0.98
517 518 5.756347 TGTGTAGTGTCAAAAACGCTCTTAT 59.244 36.000 0.00 0.00 45.69 1.73
518 519 5.110598 TGTGTAGTGTCAAAAACGCTCTTA 58.889 37.500 0.00 0.00 45.69 2.10
519 520 3.936453 TGTGTAGTGTCAAAAACGCTCTT 59.064 39.130 0.00 0.00 45.69 2.85
520 521 3.527533 TGTGTAGTGTCAAAAACGCTCT 58.472 40.909 0.00 0.00 45.69 4.09
521 522 3.936902 TGTGTAGTGTCAAAAACGCTC 57.063 42.857 0.00 0.00 45.69 5.03
523 524 4.011058 ACTTGTGTAGTGTCAAAAACGC 57.989 40.909 0.00 0.00 35.19 4.84
534 535 3.687698 AGCGTTTTTGACACTTGTGTAGT 59.312 39.130 6.37 0.00 37.68 2.73
535 536 4.271687 GAGCGTTTTTGACACTTGTGTAG 58.728 43.478 6.37 0.00 0.00 2.74
536 537 3.064271 GGAGCGTTTTTGACACTTGTGTA 59.936 43.478 6.37 0.00 0.00 2.90
537 538 2.159435 GGAGCGTTTTTGACACTTGTGT 60.159 45.455 6.06 6.06 0.00 3.72
538 539 2.450160 GGAGCGTTTTTGACACTTGTG 58.550 47.619 0.00 0.00 0.00 3.33
539 540 1.063469 CGGAGCGTTTTTGACACTTGT 59.937 47.619 0.00 0.00 0.00 3.16
540 541 1.063469 ACGGAGCGTTTTTGACACTTG 59.937 47.619 0.00 0.00 36.35 3.16
541 542 1.329599 GACGGAGCGTTTTTGACACTT 59.670 47.619 0.00 0.00 41.37 3.16
542 543 0.935196 GACGGAGCGTTTTTGACACT 59.065 50.000 0.00 0.00 41.37 3.55
543 544 0.041576 GGACGGAGCGTTTTTGACAC 60.042 55.000 0.00 0.00 41.37 3.67
544 545 1.161563 GGGACGGAGCGTTTTTGACA 61.162 55.000 0.00 0.00 41.37 3.58
545 546 1.161563 TGGGACGGAGCGTTTTTGAC 61.162 55.000 0.00 0.00 41.37 3.18
546 547 0.250553 ATGGGACGGAGCGTTTTTGA 60.251 50.000 0.00 0.00 41.37 2.69
547 548 1.444836 TATGGGACGGAGCGTTTTTG 58.555 50.000 0.00 0.00 41.37 2.44
548 549 2.188062 TTATGGGACGGAGCGTTTTT 57.812 45.000 0.00 0.00 41.37 1.94
549 550 2.413310 ATTATGGGACGGAGCGTTTT 57.587 45.000 0.00 0.00 41.37 2.43
550 551 3.764237 ATATTATGGGACGGAGCGTTT 57.236 42.857 0.00 0.00 41.37 3.60
551 552 4.525487 TCTTATATTATGGGACGGAGCGTT 59.475 41.667 0.00 0.00 41.37 4.84
552 553 4.084287 TCTTATATTATGGGACGGAGCGT 58.916 43.478 0.00 0.00 45.10 5.07
553 554 4.673441 CTCTTATATTATGGGACGGAGCG 58.327 47.826 0.00 0.00 0.00 5.03
554 555 4.434520 GCTCTTATATTATGGGACGGAGC 58.565 47.826 0.00 0.00 37.19 4.70
555 556 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
556 557 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
557 558 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
558 559 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
559 560 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
560 561 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
561 562 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
562 563 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
565 566 9.642327 TGTAGTGTCAAAAACGCTCTTATATTA 57.358 29.630 0.00 0.00 45.69 0.98
566 567 8.440833 GTGTAGTGTCAAAAACGCTCTTATATT 58.559 33.333 0.00 0.00 45.69 1.28
567 568 7.601130 TGTGTAGTGTCAAAAACGCTCTTATAT 59.399 33.333 0.00 0.00 45.69 0.86
568 569 6.924612 TGTGTAGTGTCAAAAACGCTCTTATA 59.075 34.615 0.00 0.00 45.69 0.98
569 570 5.756347 TGTGTAGTGTCAAAAACGCTCTTAT 59.244 36.000 0.00 0.00 45.69 1.73
570 571 5.110598 TGTGTAGTGTCAAAAACGCTCTTA 58.889 37.500 0.00 0.00 45.69 2.10
571 572 3.936453 TGTGTAGTGTCAAAAACGCTCTT 59.064 39.130 0.00 0.00 45.69 2.85
572 573 3.527533 TGTGTAGTGTCAAAAACGCTCT 58.472 40.909 0.00 0.00 45.69 4.09
573 574 3.936902 TGTGTAGTGTCAAAAACGCTC 57.063 42.857 0.00 0.00 45.69 5.03
575 576 4.011058 ACTTGTGTAGTGTCAAAAACGC 57.989 40.909 0.00 0.00 35.19 4.84
576 577 9.872757 AAATATACTTGTGTAGTGTCAAAAACG 57.127 29.630 0.00 0.00 37.73 3.60
643 644 1.068434 CCATGACCGGCTGTTGTTTTT 59.932 47.619 0.00 0.00 0.00 1.94
644 645 0.673437 CCATGACCGGCTGTTGTTTT 59.327 50.000 0.00 0.00 0.00 2.43
645 646 1.178534 CCCATGACCGGCTGTTGTTT 61.179 55.000 0.00 0.00 0.00 2.83
646 647 1.603455 CCCATGACCGGCTGTTGTT 60.603 57.895 0.00 0.00 0.00 2.83
647 648 2.034066 CCCATGACCGGCTGTTGT 59.966 61.111 0.00 0.00 0.00 3.32
648 649 3.443045 GCCCATGACCGGCTGTTG 61.443 66.667 0.00 0.00 43.48 3.33
654 655 2.747460 CACACTGCCCATGACCGG 60.747 66.667 0.00 0.00 0.00 5.28
675 676 2.051518 GGCCATCGCAAATGGGACA 61.052 57.895 15.06 0.00 39.86 4.02
703 704 0.246635 TGCGTTACAGAAGGAGAGCC 59.753 55.000 0.00 0.00 0.00 4.70
708 709 1.336887 GCTCAGTGCGTTACAGAAGGA 60.337 52.381 0.00 0.00 0.00 3.36
709 710 1.071605 GCTCAGTGCGTTACAGAAGG 58.928 55.000 0.00 0.00 0.00 3.46
720 721 7.412346 CGGAATATATATGTTTCAGCTCAGTGC 60.412 40.741 0.00 0.00 43.29 4.40
721 722 7.063898 CCGGAATATATATGTTTCAGCTCAGTG 59.936 40.741 0.00 0.00 0.00 3.66
722 723 7.099764 CCGGAATATATATGTTTCAGCTCAGT 58.900 38.462 0.00 0.00 0.00 3.41
723 724 7.099764 ACCGGAATATATATGTTTCAGCTCAG 58.900 38.462 9.46 0.00 0.00 3.35
724 725 7.004555 ACCGGAATATATATGTTTCAGCTCA 57.995 36.000 9.46 0.00 0.00 4.26
726 727 6.149474 GCAACCGGAATATATATGTTTCAGCT 59.851 38.462 9.46 0.00 0.00 4.24
727 728 6.149474 AGCAACCGGAATATATATGTTTCAGC 59.851 38.462 9.46 0.47 0.00 4.26
728 729 7.672983 AGCAACCGGAATATATATGTTTCAG 57.327 36.000 9.46 3.37 0.00 3.02
729 730 7.521423 GCAAGCAACCGGAATATATATGTTTCA 60.521 37.037 9.46 0.00 0.00 2.69
730 731 6.801862 GCAAGCAACCGGAATATATATGTTTC 59.198 38.462 9.46 0.00 0.00 2.78
731 732 6.264292 TGCAAGCAACCGGAATATATATGTTT 59.736 34.615 9.46 0.00 0.00 2.83
732 733 5.767665 TGCAAGCAACCGGAATATATATGTT 59.232 36.000 9.46 0.00 0.00 2.71
733 734 5.312895 TGCAAGCAACCGGAATATATATGT 58.687 37.500 9.46 0.00 0.00 2.29
734 735 5.872635 CTGCAAGCAACCGGAATATATATG 58.127 41.667 9.46 0.00 0.00 1.78
772 773 0.464735 GTTTTGGGTGGGGTTTTGGC 60.465 55.000 0.00 0.00 0.00 4.52
773 774 0.181587 GGTTTTGGGTGGGGTTTTGG 59.818 55.000 0.00 0.00 0.00 3.28
785 786 2.740438 CCAAAGGCGGGGTTTTGG 59.260 61.111 1.38 1.38 45.07 3.28
817 818 4.770874 GGCGGGGAAGCGCTGTAA 62.771 66.667 12.58 0.00 38.18 2.41
1456 1504 2.979814 TGTAACCGGATGATCACCTG 57.020 50.000 9.46 0.00 0.00 4.00
1473 1521 1.831652 CTTCCACCCCGAGCTCTTGT 61.832 60.000 12.85 2.93 0.00 3.16
1626 1674 1.376609 CTTCACGGCAATACCCCTGC 61.377 60.000 0.00 0.00 39.16 4.85
1809 1860 5.546621 ATGTGTTGTAGGTGACAGTACTT 57.453 39.130 0.00 0.00 39.88 2.24
1951 2002 3.201487 TCATGAATCCTCTTGTCATGGCT 59.799 43.478 11.74 0.00 45.67 4.75
1997 2048 5.451381 CCAGCATAGCATTTCAATGATGTGT 60.451 40.000 13.80 1.85 43.13 3.72
2315 2369 2.842496 ACTTCATCTGGAGCAATCCTCA 59.158 45.455 0.00 0.00 42.62 3.86
2478 2535 7.901029 TGAATATGTGAATAGTCTCCCAGATC 58.099 38.462 0.00 0.00 0.00 2.75
2617 2677 4.054780 TGCCCAACATCGTATCTAGAAC 57.945 45.455 0.00 0.00 0.00 3.01
2637 2697 1.972872 AGGGTTCAGTTCACTGCTTG 58.027 50.000 1.74 0.00 43.46 4.01
2676 2736 6.875076 AGAGTACGCTACCTTCAATTATTGT 58.125 36.000 4.77 0.00 0.00 2.71
2841 2905 6.701841 GCAACACTTATAGATTCAGATTCCGA 59.298 38.462 0.00 0.00 0.00 4.55
3151 3215 4.279420 GGATCAGAAATTTGCATCCCTACC 59.721 45.833 0.00 0.00 0.00 3.18
3195 3259 9.928236 AATTTAATTCATTTGGTTGAACAAACG 57.072 25.926 0.00 0.00 42.51 3.60


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

AutoCloner maintained by Alex Coulton.