Multiple sequence alignment - TraesCS7D01G225000

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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 TraesCS7D01G225000 chr7D 100.000 3442 0 0 1 3442 185130310 185133751 0.000000e+00 6357.0
1 TraesCS7D01G225000 chr7D 100.000 1564 0 0 3754 5317 185134063 185135626 0.000000e+00 2889.0
2 TraesCS7D01G225000 chr7D 98.361 61 0 1 4946 5006 185134262 185134321 7.280000e-19 106.0
3 TraesCS7D01G225000 chr7D 98.361 61 0 1 3953 4012 185135255 185135315 7.280000e-19 106.0
4 TraesCS7D01G225000 chr7B 92.774 2823 156 22 289 3088 327267513 327270310 0.000000e+00 4039.0
5 TraesCS7D01G225000 chr7B 96.134 1164 32 7 3755 4907 327270634 327271795 0.000000e+00 1888.0
6 TraesCS7D01G225000 chr7B 94.340 318 16 2 5001 5317 327271804 327272120 2.230000e-133 486.0
7 TraesCS7D01G225000 chr7B 95.636 275 11 1 3156 3430 327270309 327270582 1.760000e-119 440.0
8 TraesCS7D01G225000 chr7B 95.082 61 2 1 4946 5006 327270832 327270891 1.580000e-15 95.3
9 TraesCS7D01G225000 chr7A 90.407 2679 168 39 253 2874 192662365 192665011 0.000000e+00 3441.0
10 TraesCS7D01G225000 chr7A 86.946 1195 96 19 3755 4907 192665565 192666741 0.000000e+00 1288.0
11 TraesCS7D01G225000 chr7A 89.619 472 33 14 2959 3418 192665003 192665470 2.130000e-163 586.0
12 TraesCS7D01G225000 chr6A 83.068 1506 187 39 1000 2482 106798305 106799765 0.000000e+00 1306.0
13 TraesCS7D01G225000 chr6A 85.923 547 71 6 3806 4352 106800536 106801076 3.570000e-161 579.0
14 TraesCS7D01G225000 chr6B 82.876 1495 200 37 1000 2485 169108187 169109634 0.000000e+00 1291.0
15 TraesCS7D01G225000 chr6B 85.870 552 70 5 3806 4352 169110432 169110980 9.930000e-162 580.0
16 TraesCS7D01G225000 chr6B 94.521 73 2 2 3087 3157 279184574 279184502 1.570000e-20 111.0
17 TraesCS7D01G225000 chr6D 82.715 1510 194 37 1000 2485 88774935 88776401 0.000000e+00 1280.0
18 TraesCS7D01G225000 chr6D 79.728 957 128 40 1103 2045 5762615 5761711 2.700000e-177 632.0
19 TraesCS7D01G225000 chr6D 87.154 397 42 9 2694 3087 88776620 88777010 4.890000e-120 442.0
20 TraesCS7D01G225000 chr6D 89.062 320 35 0 4033 4352 88777714 88778033 1.070000e-106 398.0
21 TraesCS7D01G225000 chr6D 81.006 179 29 4 5140 5317 347301120 347300946 2.580000e-28 137.0
22 TraesCS7D01G225000 chr2A 80.597 268 47 4 5052 5317 741240154 741239890 9.030000e-48 202.0
23 TraesCS7D01G225000 chr2A 81.013 158 28 1 5154 5311 747687809 747687964 2.010000e-24 124.0
24 TraesCS7D01G225000 chr2A 85.965 114 16 0 5202 5315 733448464 733448577 7.230000e-24 122.0
25 TraesCS7D01G225000 chr1B 84.358 179 22 5 5140 5317 282129031 282128858 2.550000e-38 171.0
26 TraesCS7D01G225000 chr1B 88.889 81 5 2 3082 3158 439121168 439121248 4.380000e-16 97.1
27 TraesCS7D01G225000 chr5D 82.320 181 17 8 5140 5317 426018466 426018634 5.550000e-30 143.0
28 TraesCS7D01G225000 chr5D 100.000 30 0 0 5046 5075 43755788 43755817 7.440000e-04 56.5
29 TraesCS7D01G225000 chr3D 87.500 120 13 2 5199 5316 410375507 410375626 2.580000e-28 137.0
30 TraesCS7D01G225000 chr3D 85.542 83 8 4 3080 3158 409015476 409015394 3.410000e-12 84.2
31 TraesCS7D01G225000 chr1D 87.500 112 12 2 5207 5317 465110014 465109904 1.550000e-25 128.0
32 TraesCS7D01G225000 chr1D 87.719 57 5 2 5046 5101 395031376 395031321 1.240000e-06 65.8
33 TraesCS7D01G225000 chr2B 80.714 140 26 1 1103 1242 755624891 755624753 2.020000e-19 108.0
34 TraesCS7D01G225000 chr2B 92.308 78 1 2 3085 3157 514348605 514348528 7.280000e-19 106.0
35 TraesCS7D01G225000 chr4B 92.105 76 4 2 3084 3157 4715105 4715180 7.280000e-19 106.0
36 TraesCS7D01G225000 chr5B 92.000 75 2 2 3084 3157 692012664 692012735 9.420000e-18 102.0
37 TraesCS7D01G225000 chr2D 87.654 81 6 3 3083 3159 586574587 586574667 2.040000e-14 91.6
38 TraesCS7D01G225000 chr2D 87.179 78 5 4 3081 3157 334331505 334331578 3.410000e-12 84.2
39 TraesCS7D01G225000 chr5A 88.158 76 7 2 3084 3157 680202256 680202181 7.330000e-14 89.8
40 TraesCS7D01G225000 chr1A 89.286 56 4 2 5046 5100 489321078 489321024 9.560000e-08 69.4
41 TraesCS7D01G225000 chr1A 87.719 57 5 2 5046 5101 489379472 489379417 1.240000e-06 65.8
42 TraesCS7D01G225000 chr1A 100.000 30 0 0 5046 5075 70695182 70695211 7.440000e-04 56.5
43 TraesCS7D01G225000 chr4D 100.000 30 0 0 5045 5074 419344355 419344384 7.440000e-04 56.5
44 TraesCS7D01G225000 chr4D 96.970 33 0 1 5043 5074 277387341 277387309 3.000000e-03 54.7


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 TraesCS7D01G225000 chr7D 185130310 185135626 5316 False 2364.500000 6357 99.180500 1 5317 4 chr7D.!!$F1 5316
1 TraesCS7D01G225000 chr7B 327267513 327272120 4607 False 1389.660000 4039 94.793200 289 5317 5 chr7B.!!$F1 5028
2 TraesCS7D01G225000 chr7A 192662365 192666741 4376 False 1771.666667 3441 88.990667 253 4907 3 chr7A.!!$F1 4654
3 TraesCS7D01G225000 chr6A 106798305 106801076 2771 False 942.500000 1306 84.495500 1000 4352 2 chr6A.!!$F1 3352
4 TraesCS7D01G225000 chr6B 169108187 169110980 2793 False 935.500000 1291 84.373000 1000 4352 2 chr6B.!!$F1 3352
5 TraesCS7D01G225000 chr6D 88774935 88778033 3098 False 706.666667 1280 86.310333 1000 4352 3 chr6D.!!$F1 3352
6 TraesCS7D01G225000 chr6D 5761711 5762615 904 True 632.000000 632 79.728000 1103 2045 1 chr6D.!!$R1 942

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
808 834 0.388134 CTGCAGCAGTGGCATTTCAC 60.388 55.0 14.90 0.00 44.61 3.18 F
1344 1383 0.729690 GCATCCTTCTTTCACTCCGC 59.270 55.0 0.00 0.00 0.00 5.54 F
1945 2011 0.173481 GATGGTGAGCTGCGACAGTA 59.827 55.0 0.00 0.00 33.43 2.74 F
2996 3216 0.345502 TGGGGGTAGTTGATAGGCCT 59.654 55.0 11.78 11.78 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1753 0.041047 CACATGTCACTGGCACAACG 60.041 55.0 0.00 0.0 38.70 4.10 R
3139 3359 0.410663 TCTACTCCCTCCGTCCCAAA 59.589 55.0 0.00 0.0 0.00 3.28 R
3753 3993 0.952497 ACGACGCGTCTTAGACAGGA 60.952 55.0 33.94 0.0 33.69 3.86 R
4907 5388 0.234365 TAACCGTTAACGTTTGCGCC 59.766 50.0 25.15 0.0 42.83 6.53 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
33 34 5.798910 CAAAATATCTTTGCATTTTCCGCC 58.201 37.500 0.00 0.00 33.23 6.13
34 35 5.343307 AAATATCTTTGCATTTTCCGCCT 57.657 34.783 0.00 0.00 0.00 5.52
35 36 2.947448 ATCTTTGCATTTTCCGCCTC 57.053 45.000 0.00 0.00 0.00 4.70
36 37 1.614996 TCTTTGCATTTTCCGCCTCA 58.385 45.000 0.00 0.00 0.00 3.86
37 38 1.269448 TCTTTGCATTTTCCGCCTCAC 59.731 47.619 0.00 0.00 0.00 3.51
38 39 1.000385 CTTTGCATTTTCCGCCTCACA 60.000 47.619 0.00 0.00 0.00 3.58
39 40 1.255882 TTGCATTTTCCGCCTCACAT 58.744 45.000 0.00 0.00 0.00 3.21
40 41 1.255882 TGCATTTTCCGCCTCACATT 58.744 45.000 0.00 0.00 0.00 2.71
41 42 1.617850 TGCATTTTCCGCCTCACATTT 59.382 42.857 0.00 0.00 0.00 2.32
42 43 2.036992 TGCATTTTCCGCCTCACATTTT 59.963 40.909 0.00 0.00 0.00 1.82
43 44 3.256879 TGCATTTTCCGCCTCACATTTTA 59.743 39.130 0.00 0.00 0.00 1.52
44 45 4.081752 TGCATTTTCCGCCTCACATTTTAT 60.082 37.500 0.00 0.00 0.00 1.40
45 46 4.869861 GCATTTTCCGCCTCACATTTTATT 59.130 37.500 0.00 0.00 0.00 1.40
46 47 5.351189 GCATTTTCCGCCTCACATTTTATTT 59.649 36.000 0.00 0.00 0.00 1.40
47 48 6.533367 GCATTTTCCGCCTCACATTTTATTTA 59.467 34.615 0.00 0.00 0.00 1.40
48 49 7.464045 GCATTTTCCGCCTCACATTTTATTTAC 60.464 37.037 0.00 0.00 0.00 2.01
49 50 6.827586 TTTCCGCCTCACATTTTATTTACT 57.172 33.333 0.00 0.00 0.00 2.24
50 51 6.827586 TTCCGCCTCACATTTTATTTACTT 57.172 33.333 0.00 0.00 0.00 2.24
51 52 6.827586 TCCGCCTCACATTTTATTTACTTT 57.172 33.333 0.00 0.00 0.00 2.66
52 53 7.222000 TCCGCCTCACATTTTATTTACTTTT 57.778 32.000 0.00 0.00 0.00 2.27
53 54 7.662897 TCCGCCTCACATTTTATTTACTTTTT 58.337 30.769 0.00 0.00 0.00 1.94
54 55 7.596995 TCCGCCTCACATTTTATTTACTTTTTG 59.403 33.333 0.00 0.00 0.00 2.44
55 56 7.596995 CCGCCTCACATTTTATTTACTTTTTGA 59.403 33.333 0.00 0.00 0.00 2.69
56 57 8.973378 CGCCTCACATTTTATTTACTTTTTGAA 58.027 29.630 0.00 0.00 0.00 2.69
72 73 9.280174 TACTTTTTGAAGTTATCCACTAGTTGG 57.720 33.333 0.00 0.00 39.28 3.77
73 74 6.569179 TTTTGAAGTTATCCACTAGTTGGC 57.431 37.500 0.00 0.00 46.47 4.52
74 75 4.216411 TGAAGTTATCCACTAGTTGGCC 57.784 45.455 0.00 0.00 46.47 5.36
75 76 3.585289 TGAAGTTATCCACTAGTTGGCCA 59.415 43.478 0.00 0.00 46.47 5.36
76 77 3.629142 AGTTATCCACTAGTTGGCCAC 57.371 47.619 3.88 0.00 46.47 5.01
77 78 2.910319 AGTTATCCACTAGTTGGCCACA 59.090 45.455 3.88 0.00 46.47 4.17
78 79 3.523564 AGTTATCCACTAGTTGGCCACAT 59.476 43.478 3.88 0.00 46.47 3.21
79 80 4.018415 AGTTATCCACTAGTTGGCCACATT 60.018 41.667 3.88 0.00 46.47 2.71
80 81 2.969821 TCCACTAGTTGGCCACATTT 57.030 45.000 3.88 0.00 46.47 2.32
81 82 2.513753 TCCACTAGTTGGCCACATTTG 58.486 47.619 3.88 0.00 46.47 2.32
82 83 2.158534 TCCACTAGTTGGCCACATTTGT 60.159 45.455 3.88 0.00 46.47 2.83
83 84 2.030007 CCACTAGTTGGCCACATTTGTG 60.030 50.000 3.88 11.34 39.07 3.33
94 95 3.302365 CACATTTGTGGCCCTTGTAAG 57.698 47.619 0.00 0.00 42.10 2.34
95 96 2.627699 CACATTTGTGGCCCTTGTAAGT 59.372 45.455 0.00 0.00 42.10 2.24
96 97 3.823873 CACATTTGTGGCCCTTGTAAGTA 59.176 43.478 0.00 0.00 42.10 2.24
97 98 3.824443 ACATTTGTGGCCCTTGTAAGTAC 59.176 43.478 0.00 0.00 0.00 2.73
98 99 3.868619 TTTGTGGCCCTTGTAAGTACT 57.131 42.857 0.00 0.00 0.00 2.73
99 100 4.978438 TTTGTGGCCCTTGTAAGTACTA 57.022 40.909 0.00 0.00 0.00 1.82
100 101 3.967332 TGTGGCCCTTGTAAGTACTAC 57.033 47.619 0.00 0.00 0.00 2.73
101 102 2.568509 TGTGGCCCTTGTAAGTACTACC 59.431 50.000 0.00 0.00 0.00 3.18
102 103 2.836372 GTGGCCCTTGTAAGTACTACCT 59.164 50.000 0.00 0.00 0.00 3.08
103 104 3.102204 TGGCCCTTGTAAGTACTACCTC 58.898 50.000 0.00 0.00 0.00 3.85
104 105 3.245875 TGGCCCTTGTAAGTACTACCTCT 60.246 47.826 0.00 0.00 0.00 3.69
105 106 3.132467 GGCCCTTGTAAGTACTACCTCTG 59.868 52.174 0.00 0.00 0.00 3.35
106 107 3.768215 GCCCTTGTAAGTACTACCTCTGT 59.232 47.826 0.00 0.00 0.00 3.41
107 108 4.142204 GCCCTTGTAAGTACTACCTCTGTC 60.142 50.000 0.00 0.00 0.00 3.51
108 109 5.262804 CCCTTGTAAGTACTACCTCTGTCT 58.737 45.833 0.00 0.00 0.00 3.41
109 110 5.715753 CCCTTGTAAGTACTACCTCTGTCTT 59.284 44.000 0.00 0.00 0.00 3.01
110 111 6.210984 CCCTTGTAAGTACTACCTCTGTCTTT 59.789 42.308 0.00 0.00 0.00 2.52
111 112 7.395489 CCCTTGTAAGTACTACCTCTGTCTTTA 59.605 40.741 0.00 0.00 0.00 1.85
112 113 8.800332 CCTTGTAAGTACTACCTCTGTCTTTAA 58.200 37.037 0.00 0.00 0.00 1.52
120 121 9.085250 GTACTACCTCTGTCTTTAAATGTAAGC 57.915 37.037 0.00 0.00 0.00 3.09
121 122 7.908453 ACTACCTCTGTCTTTAAATGTAAGCT 58.092 34.615 0.00 0.00 0.00 3.74
122 123 7.819900 ACTACCTCTGTCTTTAAATGTAAGCTG 59.180 37.037 0.00 0.00 0.00 4.24
123 124 6.534634 ACCTCTGTCTTTAAATGTAAGCTGT 58.465 36.000 0.00 0.00 0.00 4.40
124 125 6.998673 ACCTCTGTCTTTAAATGTAAGCTGTT 59.001 34.615 0.00 0.00 0.00 3.16
125 126 7.173390 ACCTCTGTCTTTAAATGTAAGCTGTTC 59.827 37.037 0.00 0.00 0.00 3.18
126 127 7.173218 CCTCTGTCTTTAAATGTAAGCTGTTCA 59.827 37.037 0.00 0.00 0.00 3.18
127 128 8.445275 TCTGTCTTTAAATGTAAGCTGTTCAA 57.555 30.769 0.00 0.00 0.00 2.69
128 129 8.559536 TCTGTCTTTAAATGTAAGCTGTTCAAG 58.440 33.333 0.00 0.00 0.00 3.02
142 143 5.551760 CTGTTCAAGCAGTTCGGATTAAT 57.448 39.130 0.00 0.00 0.00 1.40
143 144 5.545658 TGTTCAAGCAGTTCGGATTAATC 57.454 39.130 6.93 6.93 0.00 1.75
144 145 4.394920 TGTTCAAGCAGTTCGGATTAATCC 59.605 41.667 22.63 22.63 43.65 3.01
155 156 3.060978 GGATTAATCCGCCAAAACGTC 57.939 47.619 18.61 0.00 37.19 4.34
156 157 2.681344 GGATTAATCCGCCAAAACGTCT 59.319 45.455 18.61 0.00 37.19 4.18
157 158 3.128068 GGATTAATCCGCCAAAACGTCTT 59.872 43.478 18.61 0.00 37.19 3.01
158 159 4.333372 GGATTAATCCGCCAAAACGTCTTA 59.667 41.667 18.61 0.00 37.19 2.10
159 160 4.666928 TTAATCCGCCAAAACGTCTTAC 57.333 40.909 0.00 0.00 0.00 2.34
160 161 2.172851 ATCCGCCAAAACGTCTTACA 57.827 45.000 0.00 0.00 0.00 2.41
161 162 2.172851 TCCGCCAAAACGTCTTACAT 57.827 45.000 0.00 0.00 0.00 2.29
162 163 2.496111 TCCGCCAAAACGTCTTACATT 58.504 42.857 0.00 0.00 0.00 2.71
163 164 2.879646 TCCGCCAAAACGTCTTACATTT 59.120 40.909 0.00 0.00 0.00 2.32
164 165 4.063689 TCCGCCAAAACGTCTTACATTTA 58.936 39.130 0.00 0.00 0.00 1.40
165 166 4.696402 TCCGCCAAAACGTCTTACATTTAT 59.304 37.500 0.00 0.00 0.00 1.40
166 167 5.025826 CCGCCAAAACGTCTTACATTTATC 58.974 41.667 0.00 0.00 0.00 1.75
167 168 5.163794 CCGCCAAAACGTCTTACATTTATCT 60.164 40.000 0.00 0.00 0.00 1.98
168 169 6.036300 CCGCCAAAACGTCTTACATTTATCTA 59.964 38.462 0.00 0.00 0.00 1.98
169 170 6.898189 CGCCAAAACGTCTTACATTTATCTAC 59.102 38.462 0.00 0.00 0.00 2.59
170 171 7.201496 CGCCAAAACGTCTTACATTTATCTACT 60.201 37.037 0.00 0.00 0.00 2.57
171 172 9.090692 GCCAAAACGTCTTACATTTATCTACTA 57.909 33.333 0.00 0.00 0.00 1.82
229 230 7.683437 AAAATGGGAAGTTGCTAGTAACTAC 57.317 36.000 24.09 19.19 39.86 2.73
230 231 6.622427 AATGGGAAGTTGCTAGTAACTACT 57.378 37.500 24.09 11.58 39.86 2.57
231 232 5.401531 TGGGAAGTTGCTAGTAACTACTG 57.598 43.478 24.09 0.00 39.86 2.74
232 233 4.836736 TGGGAAGTTGCTAGTAACTACTGT 59.163 41.667 24.09 10.54 39.86 3.55
233 234 6.012113 TGGGAAGTTGCTAGTAACTACTGTA 58.988 40.000 24.09 9.35 39.86 2.74
234 235 6.071728 TGGGAAGTTGCTAGTAACTACTGTAC 60.072 42.308 24.09 10.98 39.86 2.90
235 236 6.152492 GGGAAGTTGCTAGTAACTACTGTACT 59.848 42.308 24.09 8.82 39.86 2.73
236 237 7.337942 GGGAAGTTGCTAGTAACTACTGTACTA 59.662 40.741 24.09 0.00 39.86 1.82
237 238 8.180920 GGAAGTTGCTAGTAACTACTGTACTAC 58.819 40.741 24.09 6.26 39.86 2.73
238 239 8.627208 AAGTTGCTAGTAACTACTGTACTACA 57.373 34.615 24.09 0.00 39.86 2.74
239 240 8.038492 AGTTGCTAGTAACTACTGTACTACAC 57.962 38.462 22.82 0.00 39.03 2.90
240 241 7.663081 AGTTGCTAGTAACTACTGTACTACACA 59.337 37.037 22.82 0.00 39.03 3.72
241 242 8.457261 GTTGCTAGTAACTACTGTACTACACAT 58.543 37.037 15.60 0.00 36.29 3.21
242 243 9.671279 TTGCTAGTAACTACTGTACTACACATA 57.329 33.333 0.00 0.00 36.29 2.29
243 244 9.671279 TGCTAGTAACTACTGTACTACACATAA 57.329 33.333 0.00 0.00 36.29 1.90
273 274 8.433421 TTTAGGGTGAAATTATCTTTAGCGAG 57.567 34.615 0.00 0.00 0.00 5.03
286 287 5.113383 TCTTTAGCGAGTTGACTTTTGACA 58.887 37.500 0.00 0.00 0.00 3.58
321 327 6.382869 AATATTCCTGCAGAACATTGTAGC 57.617 37.500 17.39 0.00 37.29 3.58
327 333 4.497006 CCTGCAGAACATTGTAGCATTAGC 60.497 45.833 17.39 0.00 42.56 3.09
352 358 8.624776 GCTTTATATACTGAAGGAACAAATGCT 58.375 33.333 0.00 0.00 0.00 3.79
355 361 7.715265 ATATACTGAAGGAACAAATGCTACG 57.285 36.000 0.00 0.00 0.00 3.51
359 365 2.450609 AGGAACAAATGCTACGACGT 57.549 45.000 5.52 5.52 0.00 4.34
428 442 1.281656 CCGAGCCGTTGGTTTTGAC 59.718 57.895 0.00 0.00 0.00 3.18
607 621 2.643790 CGTCGTCGTCGTCATCCG 60.644 66.667 3.67 0.00 38.33 4.18
807 833 1.961378 CTGCAGCAGTGGCATTTCA 59.039 52.632 14.90 0.00 44.61 2.69
808 834 0.388134 CTGCAGCAGTGGCATTTCAC 60.388 55.000 14.90 0.00 44.61 3.18
826 852 3.698029 CACTTTTGTGTTCAGTCTGGG 57.302 47.619 0.00 0.00 44.94 4.45
827 853 2.024414 ACTTTTGTGTTCAGTCTGGGC 58.976 47.619 0.00 0.00 0.00 5.36
828 854 1.002468 CTTTTGTGTTCAGTCTGGGCG 60.002 52.381 0.00 0.00 0.00 6.13
829 855 0.817634 TTTGTGTTCAGTCTGGGCGG 60.818 55.000 0.00 0.00 0.00 6.13
856 886 3.372025 GCCATGGTGGTTTCCTCTTATCT 60.372 47.826 14.67 0.00 40.46 1.98
870 900 4.529446 CTCTTATCTCCGCGAGACTTAAC 58.471 47.826 8.23 0.00 41.76 2.01
911 941 1.448540 CAACCGAATCGCAGCCTCT 60.449 57.895 0.00 0.00 0.00 3.69
1136 1175 2.509336 CGCGCTCAGAACCCGAAT 60.509 61.111 5.56 0.00 0.00 3.34
1194 1233 4.144703 GAGGAACGAGGGGGCGTC 62.145 72.222 0.00 0.00 44.86 5.19
1197 1236 4.790861 GAACGAGGGGGCGTCGAC 62.791 72.222 5.18 5.18 44.86 4.20
1328 1367 4.592192 CGCCATCGAGGTCCGCAT 62.592 66.667 0.00 0.00 40.61 4.73
1344 1383 0.729690 GCATCCTTCTTTCACTCCGC 59.270 55.000 0.00 0.00 0.00 5.54
1357 1396 2.032376 TCCGCTGTGCAATGCTGA 59.968 55.556 6.82 6.45 0.00 4.26
1514 1561 2.949177 TAGAAGCTGGCAGGAAAACA 57.051 45.000 17.64 0.00 0.00 2.83
1562 1610 9.791801 TTCACTTGGCATTATATAGCTTTCATA 57.208 29.630 0.00 0.00 0.00 2.15
1563 1611 9.964354 TCACTTGGCATTATATAGCTTTCATAT 57.036 29.630 0.00 0.00 0.00 1.78
1698 1753 6.822667 TTGTGGCATATGGTTCATATCATC 57.177 37.500 4.56 0.00 35.18 2.92
1860 1921 3.054361 AGCTCCGTATCCTGGAACAAAAT 60.054 43.478 0.00 0.00 38.70 1.82
1944 2010 1.079543 GATGGTGAGCTGCGACAGT 60.080 57.895 0.00 0.00 33.43 3.55
1945 2011 0.173481 GATGGTGAGCTGCGACAGTA 59.827 55.000 0.00 0.00 33.43 2.74
1946 2012 0.608130 ATGGTGAGCTGCGACAGTAA 59.392 50.000 0.00 0.00 33.43 2.24
1947 2013 0.391228 TGGTGAGCTGCGACAGTAAA 59.609 50.000 0.00 0.00 33.43 2.01
1951 2017 3.682858 GGTGAGCTGCGACAGTAAATAAA 59.317 43.478 0.00 0.00 33.43 1.40
2029 2095 7.977293 ACTTAAGTTTTGGTGTTGTTGGTAATC 59.023 33.333 1.12 0.00 0.00 1.75
2047 2117 6.966751 GGTAATCTACCCTTTTTCCCTTAGT 58.033 40.000 0.00 0.00 43.18 2.24
2142 2215 6.269315 GTTCATTCGTCATGACTCAGTAGAT 58.731 40.000 22.95 4.39 41.98 1.98
2236 2322 1.072331 GAGGTGAGGAAAGGTGAAGCA 59.928 52.381 0.00 0.00 0.00 3.91
2324 2410 1.416030 TGCAGCTGTAACTTCCACTCA 59.584 47.619 16.64 0.00 0.00 3.41
2325 2411 2.072298 GCAGCTGTAACTTCCACTCAG 58.928 52.381 16.64 0.00 0.00 3.35
2552 2657 7.484035 AGAGTTAGGTCATTGATATTTTCGC 57.516 36.000 0.00 0.00 0.00 4.70
2638 2836 8.693542 ATTTTAATAGTTGCAAATCTCTGTGC 57.306 30.769 1.02 0.00 41.29 4.57
2673 2871 7.213178 ACACCTGTTAGATATCCTTTGGAAT 57.787 36.000 0.00 0.00 34.34 3.01
2676 2874 9.627123 CACCTGTTAGATATCCTTTGGAATAAA 57.373 33.333 0.00 0.00 34.34 1.40
2697 2898 9.709495 AATAAATTTCTTTGCTTGCACAATAGA 57.291 25.926 0.00 0.00 0.00 1.98
2698 2899 7.647907 AAATTTCTTTGCTTGCACAATAGAG 57.352 32.000 0.00 0.00 0.00 2.43
2699 2900 4.771590 TTCTTTGCTTGCACAATAGAGG 57.228 40.909 0.00 0.00 0.00 3.69
2742 2943 7.870445 TCCTTATCACAAAATTACCAAGCAAAC 59.130 33.333 0.00 0.00 0.00 2.93
2834 3035 2.803030 ATCTCTTCTGGCAAGCACAT 57.197 45.000 0.00 0.00 0.00 3.21
2899 3101 2.739292 TGACTGAACGAAACTTCCTCG 58.261 47.619 0.00 0.00 42.06 4.63
2996 3216 0.345502 TGGGGGTAGTTGATAGGCCT 59.654 55.000 11.78 11.78 0.00 5.19
3102 3322 1.835531 GAAATACTCCCTCCGTCCCAA 59.164 52.381 0.00 0.00 0.00 4.12
3106 3326 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3107 3327 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3109 3329 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3112 3332 3.560453 CCCTCCGTCCCAAAATAAGTGAA 60.560 47.826 0.00 0.00 0.00 3.18
3113 3333 4.270008 CCTCCGTCCCAAAATAAGTGAAT 58.730 43.478 0.00 0.00 0.00 2.57
3114 3334 4.335594 CCTCCGTCCCAAAATAAGTGAATC 59.664 45.833 0.00 0.00 0.00 2.52
3115 3335 4.912586 TCCGTCCCAAAATAAGTGAATCA 58.087 39.130 0.00 0.00 0.00 2.57
3116 3336 5.317808 TCCGTCCCAAAATAAGTGAATCAA 58.682 37.500 0.00 0.00 0.00 2.57
3117 3337 5.182380 TCCGTCCCAAAATAAGTGAATCAAC 59.818 40.000 0.00 0.00 0.00 3.18
3119 3339 6.314784 CGTCCCAAAATAAGTGAATCAACTC 58.685 40.000 0.00 0.00 0.00 3.01
3120 3340 6.149474 CGTCCCAAAATAAGTGAATCAACTCT 59.851 38.462 0.00 0.00 0.00 3.24
3122 3342 8.451748 GTCCCAAAATAAGTGAATCAACTCTAC 58.548 37.037 0.00 0.00 0.00 2.59
3123 3343 8.160765 TCCCAAAATAAGTGAATCAACTCTACA 58.839 33.333 0.00 0.00 0.00 2.74
3124 3344 8.792633 CCCAAAATAAGTGAATCAACTCTACAA 58.207 33.333 0.00 0.00 0.00 2.41
3355 3584 9.658799 CTTTATTCCTCAATTCAGACTTAGTCA 57.341 33.333 15.23 0.00 34.60 3.41
3406 3635 0.955428 ACAGCCCAACACATGCTACG 60.955 55.000 0.00 0.00 33.16 3.51
3423 3663 2.629656 CGCTGCCCCCACTTTTCAG 61.630 63.158 0.00 0.00 0.00 3.02
3433 3673 3.888930 CCCCACTTTTCAGAGCTTAACAA 59.111 43.478 0.00 0.00 0.00 2.83
3795 4035 1.875514 CGCATGACGGATCATTTCCAT 59.124 47.619 0.00 0.00 43.40 3.41
3897 4137 5.186198 GGAGCTTGTGGATATGTGTTAGTT 58.814 41.667 0.00 0.00 0.00 2.24
4077 4513 3.398920 CGGCTGGTATGAACGCAG 58.601 61.111 0.00 0.00 0.00 5.18
4131 4575 7.342284 TCTTTGGGACACTGGTAATTTTTAACA 59.658 33.333 0.00 0.00 39.29 2.41
4339 4783 2.365617 AGGTAGAATGCCACCATACTCG 59.634 50.000 0.00 0.00 46.86 4.18
4352 4796 5.467399 CCACCATACTCGTTTGTAGTTGAAA 59.533 40.000 0.00 0.00 0.00 2.69
4358 4802 6.490566 ACTCGTTTGTAGTTGAAAGTTTGT 57.509 33.333 0.00 0.00 0.00 2.83
4387 4831 5.067674 TGACTGAACTTGCAGCATTTTAGTT 59.932 36.000 9.53 9.53 39.51 2.24
4416 4860 1.014804 AAATGCTCCCCCATTACCCA 58.985 50.000 0.00 0.00 34.50 4.51
4591 5044 1.079750 GTCCCAGTCACGCCTTCTC 60.080 63.158 0.00 0.00 0.00 2.87
4634 5095 4.454504 TGCATTCTCTTAACCTTTTCCGTC 59.545 41.667 0.00 0.00 0.00 4.79
4666 5129 6.943899 TTTAAATTTTGGGGGCATTACTCT 57.056 33.333 0.00 0.00 0.00 3.24
4841 5322 2.156697 GCTTTGCTCTCACGAACTCTTC 59.843 50.000 0.00 0.00 0.00 2.87
4907 5388 2.481952 GCCAGGAATAATGCTTAGCGAG 59.518 50.000 0.00 0.00 0.00 5.03
4908 5389 3.070018 CCAGGAATAATGCTTAGCGAGG 58.930 50.000 0.00 0.00 0.00 4.63
4909 5390 2.481952 CAGGAATAATGCTTAGCGAGGC 59.518 50.000 0.00 0.00 0.00 4.70
4921 5402 4.410252 CGAGGCGCAAACGTTAAC 57.590 55.556 10.83 0.00 42.83 2.01
4922 5403 1.506277 CGAGGCGCAAACGTTAACG 60.506 57.895 25.68 25.68 46.33 3.18
4923 5404 1.154543 GAGGCGCAAACGTTAACGG 60.155 57.895 29.81 14.70 44.95 4.44
4924 5405 1.834458 GAGGCGCAAACGTTAACGGT 61.834 55.000 29.81 23.08 43.60 4.83
4933 5414 2.747396 ACGTTAACGGTTATGGCAGA 57.253 45.000 29.81 0.00 44.95 4.26
4934 5415 2.613691 ACGTTAACGGTTATGGCAGAG 58.386 47.619 29.81 0.07 44.95 3.35
4935 5416 2.028748 ACGTTAACGGTTATGGCAGAGT 60.029 45.455 29.81 3.10 44.95 3.24
4936 5417 2.997986 CGTTAACGGTTATGGCAGAGTT 59.002 45.455 20.24 0.00 35.37 3.01
4937 5418 3.434299 CGTTAACGGTTATGGCAGAGTTT 59.566 43.478 20.24 0.00 35.37 2.66
4938 5419 4.626604 CGTTAACGGTTATGGCAGAGTTTA 59.373 41.667 20.24 0.00 35.37 2.01
4939 5420 5.220340 CGTTAACGGTTATGGCAGAGTTTAG 60.220 44.000 20.24 0.00 35.37 1.85
4940 5421 4.546829 AACGGTTATGGCAGAGTTTAGA 57.453 40.909 0.00 0.00 0.00 2.10
4941 5422 4.546829 ACGGTTATGGCAGAGTTTAGAA 57.453 40.909 0.00 0.00 0.00 2.10
4942 5423 4.901868 ACGGTTATGGCAGAGTTTAGAAA 58.098 39.130 0.00 0.00 0.00 2.52
4943 5424 5.310451 ACGGTTATGGCAGAGTTTAGAAAA 58.690 37.500 0.00 0.00 0.00 2.29
4944 5425 5.411669 ACGGTTATGGCAGAGTTTAGAAAAG 59.588 40.000 0.00 0.00 0.00 2.27
4945 5426 5.642063 CGGTTATGGCAGAGTTTAGAAAAGA 59.358 40.000 0.00 0.00 0.00 2.52
4946 5427 6.316390 CGGTTATGGCAGAGTTTAGAAAAGAT 59.684 38.462 0.00 0.00 0.00 2.40
4947 5428 7.148239 CGGTTATGGCAGAGTTTAGAAAAGATT 60.148 37.037 0.00 0.00 0.00 2.40
4948 5429 8.184848 GGTTATGGCAGAGTTTAGAAAAGATTC 58.815 37.037 0.00 0.00 35.70 2.52
4949 5430 8.730680 GTTATGGCAGAGTTTAGAAAAGATTCA 58.269 33.333 0.00 0.00 38.06 2.57
4950 5431 6.808008 TGGCAGAGTTTAGAAAAGATTCAG 57.192 37.500 0.00 0.00 38.06 3.02
4951 5432 6.299141 TGGCAGAGTTTAGAAAAGATTCAGT 58.701 36.000 0.00 0.00 38.06 3.41
4952 5433 6.205464 TGGCAGAGTTTAGAAAAGATTCAGTG 59.795 38.462 0.00 0.00 38.06 3.66
4953 5434 6.428159 GGCAGAGTTTAGAAAAGATTCAGTGA 59.572 38.462 0.00 0.00 38.06 3.41
4954 5435 7.120432 GGCAGAGTTTAGAAAAGATTCAGTGAT 59.880 37.037 0.00 0.00 38.06 3.06
4955 5436 8.510505 GCAGAGTTTAGAAAAGATTCAGTGATT 58.489 33.333 0.00 0.00 38.06 2.57
4962 5443 9.784531 TTAGAAAAGATTCAGTGATTCTTCAGT 57.215 29.630 23.69 15.22 38.06 3.41
4963 5444 8.688747 AGAAAAGATTCAGTGATTCTTCAGTT 57.311 30.769 23.69 16.93 38.06 3.16
4964 5445 8.566260 AGAAAAGATTCAGTGATTCTTCAGTTG 58.434 33.333 23.69 0.00 38.06 3.16
4965 5446 8.455903 AAAAGATTCAGTGATTCTTCAGTTGA 57.544 30.769 23.69 0.00 33.11 3.18
4966 5447 7.670009 AAGATTCAGTGATTCTTCAGTTGAG 57.330 36.000 19.79 0.00 33.07 3.02
4967 5448 7.002250 AGATTCAGTGATTCTTCAGTTGAGA 57.998 36.000 11.02 0.00 33.07 3.27
4968 5449 7.448420 AGATTCAGTGATTCTTCAGTTGAGAA 58.552 34.615 11.02 0.00 33.07 2.87
4969 5450 7.935755 AGATTCAGTGATTCTTCAGTTGAGAAA 59.064 33.333 11.02 0.00 33.07 2.52
4970 5451 7.864108 TTCAGTGATTCTTCAGTTGAGAAAA 57.136 32.000 0.00 0.00 33.07 2.29
4971 5452 7.488187 TCAGTGATTCTTCAGTTGAGAAAAG 57.512 36.000 0.00 0.00 33.07 2.27
4972 5453 7.275183 TCAGTGATTCTTCAGTTGAGAAAAGA 58.725 34.615 0.00 0.00 33.07 2.52
4973 5454 7.935755 TCAGTGATTCTTCAGTTGAGAAAAGAT 59.064 33.333 0.00 0.00 33.07 2.40
4974 5455 8.566260 CAGTGATTCTTCAGTTGAGAAAAGATT 58.434 33.333 0.00 0.00 33.07 2.40
4975 5456 8.782144 AGTGATTCTTCAGTTGAGAAAAGATTC 58.218 33.333 0.00 0.00 31.17 2.52
4976 5457 8.782144 GTGATTCTTCAGTTGAGAAAAGATTCT 58.218 33.333 0.00 0.00 39.55 2.40
4977 5458 9.347240 TGATTCTTCAGTTGAGAAAAGATTCTT 57.653 29.630 0.00 0.00 45.91 2.52
4978 5459 9.824534 GATTCTTCAGTTGAGAAAAGATTCTTC 57.175 33.333 0.00 0.00 45.91 2.87
4979 5460 8.737168 TTCTTCAGTTGAGAAAAGATTCTTCA 57.263 30.769 0.00 0.00 45.91 3.02
4980 5461 8.737168 TCTTCAGTTGAGAAAAGATTCTTCAA 57.263 30.769 0.00 0.00 45.91 2.69
4981 5462 9.347240 TCTTCAGTTGAGAAAAGATTCTTCAAT 57.653 29.630 0.00 0.00 45.91 2.57
4982 5463 9.962783 CTTCAGTTGAGAAAAGATTCTTCAATT 57.037 29.630 0.00 0.00 45.91 2.32
5029 5510 1.727022 CTTTCTTGCAAGCGCCACG 60.727 57.895 21.99 0.00 37.32 4.94
5078 5559 1.813753 CGCGGATCACCAAACGGAT 60.814 57.895 0.00 0.00 35.59 4.18
5093 5574 1.809207 GGATGGCACCAAATGTCCG 59.191 57.895 0.00 0.00 28.68 4.79
5094 5575 1.139520 GATGGCACCAAATGTCCGC 59.860 57.895 0.00 0.00 28.68 5.54
5163 5644 2.228822 CCAACTGTAGGCACCAAATGTC 59.771 50.000 0.00 0.00 0.00 3.06
5197 5679 2.806945 TTTTCCCCATGCCTAGAGTG 57.193 50.000 0.00 0.00 0.00 3.51
5205 5687 3.378427 CCCATGCCTAGAGTGCTAAAAAC 59.622 47.826 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.581874 AGGCGGAAAATGCAAAGATATTTTG 59.418 36.000 0.00 6.19 36.81 2.44
11 12 5.733676 AGGCGGAAAATGCAAAGATATTTT 58.266 33.333 0.00 0.00 38.72 1.82
12 13 5.105392 TGAGGCGGAAAATGCAAAGATATTT 60.105 36.000 0.00 0.00 0.00 1.40
13 14 4.402155 TGAGGCGGAAAATGCAAAGATATT 59.598 37.500 0.00 0.00 0.00 1.28
14 15 3.953612 TGAGGCGGAAAATGCAAAGATAT 59.046 39.130 0.00 0.00 0.00 1.63
15 16 3.128589 GTGAGGCGGAAAATGCAAAGATA 59.871 43.478 0.00 0.00 0.00 1.98
16 17 2.094545 GTGAGGCGGAAAATGCAAAGAT 60.095 45.455 0.00 0.00 0.00 2.40
17 18 1.269448 GTGAGGCGGAAAATGCAAAGA 59.731 47.619 0.00 0.00 0.00 2.52
18 19 1.000385 TGTGAGGCGGAAAATGCAAAG 60.000 47.619 0.00 0.00 0.00 2.77
19 20 1.035923 TGTGAGGCGGAAAATGCAAA 58.964 45.000 0.00 0.00 0.00 3.68
20 21 1.255882 ATGTGAGGCGGAAAATGCAA 58.744 45.000 0.00 0.00 0.00 4.08
21 22 1.255882 AATGTGAGGCGGAAAATGCA 58.744 45.000 0.00 0.00 0.00 3.96
22 23 2.368655 AAATGTGAGGCGGAAAATGC 57.631 45.000 0.00 0.00 0.00 3.56
23 24 6.966435 AAATAAAATGTGAGGCGGAAAATG 57.034 33.333 0.00 0.00 0.00 2.32
24 25 7.836842 AGTAAATAAAATGTGAGGCGGAAAAT 58.163 30.769 0.00 0.00 0.00 1.82
25 26 7.222000 AGTAAATAAAATGTGAGGCGGAAAA 57.778 32.000 0.00 0.00 0.00 2.29
26 27 6.827586 AGTAAATAAAATGTGAGGCGGAAA 57.172 33.333 0.00 0.00 0.00 3.13
27 28 6.827586 AAGTAAATAAAATGTGAGGCGGAA 57.172 33.333 0.00 0.00 0.00 4.30
28 29 6.827586 AAAGTAAATAAAATGTGAGGCGGA 57.172 33.333 0.00 0.00 0.00 5.54
29 30 7.596995 TCAAAAAGTAAATAAAATGTGAGGCGG 59.403 33.333 0.00 0.00 0.00 6.13
30 31 8.514136 TCAAAAAGTAAATAAAATGTGAGGCG 57.486 30.769 0.00 0.00 0.00 5.52
57 58 9.644119 CACAAATGTGGCCAACTAGTGGATAAC 62.644 44.444 7.24 8.91 45.26 1.89
58 59 7.744641 CACAAATGTGGCCAACTAGTGGATAA 61.745 42.308 7.24 0.00 45.26 1.75
59 60 6.323003 CACAAATGTGGCCAACTAGTGGATA 61.323 44.000 7.24 1.39 45.26 2.59
60 61 5.588696 CACAAATGTGGCCAACTAGTGGAT 61.589 45.833 7.24 0.00 45.26 3.41
61 62 4.309492 CACAAATGTGGCCAACTAGTGGA 61.309 47.826 7.24 0.00 45.26 4.02
62 63 2.030007 CACAAATGTGGCCAACTAGTGG 60.030 50.000 7.24 1.28 42.96 4.00
63 64 3.287312 CACAAATGTGGCCAACTAGTG 57.713 47.619 7.24 9.67 42.10 2.74
74 75 2.627699 ACTTACAAGGGCCACAAATGTG 59.372 45.455 6.18 6.57 45.23 3.21
75 76 2.957474 ACTTACAAGGGCCACAAATGT 58.043 42.857 6.18 5.25 0.00 2.71
76 77 4.079253 AGTACTTACAAGGGCCACAAATG 58.921 43.478 6.18 0.00 0.00 2.32
77 78 4.382386 AGTACTTACAAGGGCCACAAAT 57.618 40.909 6.18 0.00 0.00 2.32
78 79 3.868619 AGTACTTACAAGGGCCACAAA 57.131 42.857 6.18 0.00 0.00 2.83
79 80 3.008266 GGTAGTACTTACAAGGGCCACAA 59.992 47.826 6.18 0.00 33.73 3.33
80 81 2.568509 GGTAGTACTTACAAGGGCCACA 59.431 50.000 6.18 0.00 33.73 4.17
81 82 2.836372 AGGTAGTACTTACAAGGGCCAC 59.164 50.000 6.18 0.00 33.73 5.01
82 83 3.102204 GAGGTAGTACTTACAAGGGCCA 58.898 50.000 6.18 0.00 33.73 5.36
83 84 3.132467 CAGAGGTAGTACTTACAAGGGCC 59.868 52.174 0.00 0.00 33.73 5.80
84 85 3.768215 ACAGAGGTAGTACTTACAAGGGC 59.232 47.826 0.00 0.00 33.73 5.19
85 86 5.262804 AGACAGAGGTAGTACTTACAAGGG 58.737 45.833 0.00 0.00 33.73 3.95
86 87 6.837471 AAGACAGAGGTAGTACTTACAAGG 57.163 41.667 0.00 0.00 33.73 3.61
94 95 9.085250 GCTTACATTTAAAGACAGAGGTAGTAC 57.915 37.037 0.00 0.00 0.00 2.73
95 96 9.032624 AGCTTACATTTAAAGACAGAGGTAGTA 57.967 33.333 0.00 0.00 0.00 1.82
96 97 7.819900 CAGCTTACATTTAAAGACAGAGGTAGT 59.180 37.037 0.00 0.00 0.00 2.73
97 98 7.819900 ACAGCTTACATTTAAAGACAGAGGTAG 59.180 37.037 0.00 0.00 0.00 3.18
98 99 7.676947 ACAGCTTACATTTAAAGACAGAGGTA 58.323 34.615 0.00 0.00 0.00 3.08
99 100 6.534634 ACAGCTTACATTTAAAGACAGAGGT 58.465 36.000 0.00 0.00 0.00 3.85
100 101 7.173218 TGAACAGCTTACATTTAAAGACAGAGG 59.827 37.037 0.00 0.00 0.00 3.69
101 102 8.087982 TGAACAGCTTACATTTAAAGACAGAG 57.912 34.615 0.00 0.00 0.00 3.35
102 103 8.445275 TTGAACAGCTTACATTTAAAGACAGA 57.555 30.769 0.00 0.00 0.00 3.41
103 104 7.324616 GCTTGAACAGCTTACATTTAAAGACAG 59.675 37.037 0.00 0.00 46.27 3.51
104 105 7.138736 GCTTGAACAGCTTACATTTAAAGACA 58.861 34.615 0.00 0.00 46.27 3.41
105 106 7.554243 GCTTGAACAGCTTACATTTAAAGAC 57.446 36.000 0.00 0.00 46.27 3.01
119 120 8.797739 GGATTAATCCGAACTGCTTGAACAGC 62.798 46.154 18.61 0.00 42.45 4.40
120 121 5.447818 GGATTAATCCGAACTGCTTGAACAG 60.448 44.000 18.61 0.00 39.28 3.16
121 122 4.394920 GGATTAATCCGAACTGCTTGAACA 59.605 41.667 18.61 0.00 37.19 3.18
122 123 4.909894 GGATTAATCCGAACTGCTTGAAC 58.090 43.478 18.61 0.00 37.19 3.18
135 136 2.681344 AGACGTTTTGGCGGATTAATCC 59.319 45.455 22.63 22.63 43.65 3.01
136 137 4.351131 AAGACGTTTTGGCGGATTAATC 57.649 40.909 6.93 6.93 35.98 1.75
137 138 4.696402 TGTAAGACGTTTTGGCGGATTAAT 59.304 37.500 0.83 0.00 35.98 1.40
138 139 4.063689 TGTAAGACGTTTTGGCGGATTAA 58.936 39.130 0.83 0.00 35.98 1.40
139 140 3.661944 TGTAAGACGTTTTGGCGGATTA 58.338 40.909 0.83 0.00 35.98 1.75
140 141 2.496111 TGTAAGACGTTTTGGCGGATT 58.504 42.857 0.83 0.00 35.98 3.01
141 142 2.172851 TGTAAGACGTTTTGGCGGAT 57.827 45.000 0.83 0.00 35.98 4.18
142 143 2.172851 ATGTAAGACGTTTTGGCGGA 57.827 45.000 0.83 0.00 35.98 5.54
143 144 2.981400 AATGTAAGACGTTTTGGCGG 57.019 45.000 0.83 0.00 35.98 6.13
144 145 5.864986 AGATAAATGTAAGACGTTTTGGCG 58.135 37.500 0.83 0.00 38.23 5.69
145 146 7.971455 AGTAGATAAATGTAAGACGTTTTGGC 58.029 34.615 0.83 0.00 38.23 4.52
203 204 9.392259 GTAGTTACTAGCAACTTCCCATTTTAT 57.608 33.333 13.53 0.00 39.45 1.40
204 205 8.599792 AGTAGTTACTAGCAACTTCCCATTTTA 58.400 33.333 13.53 0.00 39.45 1.52
205 206 7.390718 CAGTAGTTACTAGCAACTTCCCATTTT 59.609 37.037 13.53 0.00 39.45 1.82
206 207 6.879458 CAGTAGTTACTAGCAACTTCCCATTT 59.121 38.462 13.53 0.00 39.45 2.32
207 208 6.013639 ACAGTAGTTACTAGCAACTTCCCATT 60.014 38.462 13.53 0.00 39.45 3.16
208 209 5.484290 ACAGTAGTTACTAGCAACTTCCCAT 59.516 40.000 13.53 0.00 39.45 4.00
209 210 4.836736 ACAGTAGTTACTAGCAACTTCCCA 59.163 41.667 13.53 0.00 39.45 4.37
210 211 5.402997 ACAGTAGTTACTAGCAACTTCCC 57.597 43.478 13.53 3.31 39.45 3.97
211 212 7.155655 AGTACAGTAGTTACTAGCAACTTCC 57.844 40.000 13.53 5.56 39.45 3.46
212 213 8.725148 TGTAGTACAGTAGTTACTAGCAACTTC 58.275 37.037 13.53 8.81 39.45 3.01
213 214 8.510505 GTGTAGTACAGTAGTTACTAGCAACTT 58.489 37.037 13.53 0.00 39.45 2.66
214 215 7.663081 TGTGTAGTACAGTAGTTACTAGCAACT 59.337 37.037 12.91 12.91 37.17 3.16
215 216 7.810658 TGTGTAGTACAGTAGTTACTAGCAAC 58.189 38.462 2.39 0.00 34.13 4.17
216 217 7.984422 TGTGTAGTACAGTAGTTACTAGCAA 57.016 36.000 2.39 0.00 34.13 3.91
217 218 9.671279 TTATGTGTAGTACAGTAGTTACTAGCA 57.329 33.333 2.39 0.00 43.80 3.49
247 248 8.974060 TCGCTAAAGATAATTTCACCCTAAAT 57.026 30.769 0.00 0.00 0.00 1.40
248 249 8.044908 ACTCGCTAAAGATAATTTCACCCTAAA 58.955 33.333 0.00 0.00 0.00 1.85
249 250 7.562135 ACTCGCTAAAGATAATTTCACCCTAA 58.438 34.615 0.00 0.00 0.00 2.69
250 251 7.120923 ACTCGCTAAAGATAATTTCACCCTA 57.879 36.000 0.00 0.00 0.00 3.53
251 252 5.990668 ACTCGCTAAAGATAATTTCACCCT 58.009 37.500 0.00 0.00 0.00 4.34
260 261 7.439955 TGTCAAAAGTCAACTCGCTAAAGATAA 59.560 33.333 0.00 0.00 0.00 1.75
261 262 6.926826 TGTCAAAAGTCAACTCGCTAAAGATA 59.073 34.615 0.00 0.00 0.00 1.98
331 337 7.438459 GTCGTAGCATTTGTTCCTTCAGTATAT 59.562 37.037 0.00 0.00 0.00 0.86
335 341 3.746492 GTCGTAGCATTTGTTCCTTCAGT 59.254 43.478 0.00 0.00 0.00 3.41
342 348 3.916172 TCACTACGTCGTAGCATTTGTTC 59.084 43.478 28.07 0.00 39.51 3.18
352 358 2.608090 CTCATCAGCTCACTACGTCGTA 59.392 50.000 4.78 4.78 0.00 3.43
355 361 3.430931 GTTCTCATCAGCTCACTACGTC 58.569 50.000 0.00 0.00 0.00 4.34
359 365 1.818674 TGCGTTCTCATCAGCTCACTA 59.181 47.619 0.00 0.00 0.00 2.74
504 518 1.192428 GGAAGACCTACACCACCGAT 58.808 55.000 0.00 0.00 0.00 4.18
607 621 4.517703 CGACGACGACGAGGAGGC 62.518 72.222 15.32 0.00 42.66 4.70
807 833 2.024414 GCCCAGACTGAACACAAAAGT 58.976 47.619 3.32 0.00 0.00 2.66
808 834 1.002468 CGCCCAGACTGAACACAAAAG 60.002 52.381 3.32 0.00 0.00 2.27
833 859 0.779997 AAGAGGAAACCACCATGGCT 59.220 50.000 13.04 0.00 42.67 4.75
838 868 2.500098 CGGAGATAAGAGGAAACCACCA 59.500 50.000 0.00 0.00 0.00 4.17
856 886 2.879907 CCGGTTAAGTCTCGCGGA 59.120 61.111 6.13 0.00 0.00 5.54
892 922 3.100862 GAGGCTGCGATTCGGTTGC 62.101 63.158 8.34 0.00 37.76 4.17
1099 1138 0.323629 GTGACGGTGGATTGGAAGGA 59.676 55.000 0.00 0.00 0.00 3.36
1194 1233 1.424635 GTCTTCCTCGTCCTCGTCG 59.575 63.158 0.00 0.00 38.33 5.12
1197 1236 2.100603 GCGTCTTCCTCGTCCTCG 59.899 66.667 0.00 0.00 38.55 4.63
1328 1367 1.048601 ACAGCGGAGTGAAAGAAGGA 58.951 50.000 0.00 0.00 0.00 3.36
1344 1383 3.190744 AGAAACAGATCAGCATTGCACAG 59.809 43.478 11.91 0.37 0.00 3.66
1389 1428 5.416639 AGCTTCATGCATCAACAGTCAAATA 59.583 36.000 0.00 0.00 45.94 1.40
1514 1561 4.927049 ACCATTTGATCAGACTCACCATT 58.073 39.130 0.00 0.00 0.00 3.16
1566 1614 9.906660 CAATGCCATCAACTAAACTAAAGTAAA 57.093 29.630 0.00 0.00 0.00 2.01
1567 1615 8.026607 GCAATGCCATCAACTAAACTAAAGTAA 58.973 33.333 0.00 0.00 0.00 2.24
1698 1753 0.041047 CACATGTCACTGGCACAACG 60.041 55.000 0.00 0.00 38.70 4.10
1860 1921 4.406326 TGGGTGGTAAGATACGCTGATTTA 59.594 41.667 0.00 0.00 0.00 1.40
1931 1997 3.932710 CCTTTATTTACTGTCGCAGCTCA 59.067 43.478 6.74 0.00 34.37 4.26
1951 2017 7.336679 TGTTCGATGATTGATGAATGTTAACCT 59.663 33.333 2.48 0.00 0.00 3.50
1997 2063 9.498307 CAACAACACCAAAACTTAAGTACTAAG 57.502 33.333 8.92 3.36 42.52 2.18
2236 2322 7.340232 ACATATATGCCAACAGTGAAAGTGAAT 59.660 33.333 12.79 0.00 40.62 2.57
2240 2326 6.094048 GTGACATATATGCCAACAGTGAAAGT 59.906 38.462 12.79 0.00 0.00 2.66
2314 2400 7.881775 AAGTCAATAAAAACTGAGTGGAAGT 57.118 32.000 0.00 0.00 0.00 3.01
2459 2546 9.916360 ATGTAATCCATATGTCATCAGCAATAT 57.084 29.630 1.24 0.00 29.82 1.28
2491 2589 4.261801 CAAGGTAATGTTGTTCCGATCCT 58.738 43.478 0.00 0.00 0.00 3.24
2551 2656 9.840427 AAACTACATAGTTATGTCAAACATTGC 57.160 29.630 7.99 0.00 45.17 3.56
2638 2836 9.522804 GATATCTAACAGGTGTACAAGAAAGAG 57.477 37.037 0.00 0.00 0.00 2.85
2673 2871 7.814107 CCTCTATTGTGCAAGCAAAGAAATTTA 59.186 33.333 0.00 0.00 31.63 1.40
2676 2874 5.337009 CCCTCTATTGTGCAAGCAAAGAAAT 60.337 40.000 0.00 0.00 31.63 2.17
2697 2898 2.305052 GGACTAGCACAAAGGTAACCCT 59.695 50.000 0.00 0.00 45.63 4.34
2698 2899 2.305052 AGGACTAGCACAAAGGTAACCC 59.695 50.000 0.00 0.00 31.44 4.11
2699 2900 3.697619 AGGACTAGCACAAAGGTAACC 57.302 47.619 0.00 0.00 37.17 2.85
2742 2943 9.897744 CATAAGCATGTTTGGTATTGGTTATAG 57.102 33.333 4.89 0.17 39.45 1.31
2834 3035 2.665165 AGAAACACCAACTGGCAATGA 58.335 42.857 0.00 0.00 39.32 2.57
2899 3101 6.553857 TCTCCCACCTCTATTCTCCTATTAC 58.446 44.000 0.00 0.00 0.00 1.89
3115 3335 9.614792 AAATAAGTGACTCAACTTTGTAGAGTT 57.385 29.630 0.00 0.00 42.29 3.01
3116 3336 9.046296 CAAATAAGTGACTCAACTTTGTAGAGT 57.954 33.333 0.00 0.00 44.71 3.24
3117 3337 8.499162 CCAAATAAGTGACTCAACTTTGTAGAG 58.501 37.037 0.00 0.00 40.77 2.43
3119 3339 7.444183 TCCCAAATAAGTGACTCAACTTTGTAG 59.556 37.037 0.00 0.00 40.77 2.74
3120 3340 7.227910 GTCCCAAATAAGTGACTCAACTTTGTA 59.772 37.037 0.00 0.00 40.77 2.41
3122 3342 6.438763 GTCCCAAATAAGTGACTCAACTTTG 58.561 40.000 0.00 0.00 40.77 2.77
3123 3343 5.238650 CGTCCCAAATAAGTGACTCAACTTT 59.761 40.000 0.00 0.00 40.77 2.66
3124 3344 4.755123 CGTCCCAAATAAGTGACTCAACTT 59.245 41.667 0.00 0.00 42.89 2.66
3125 3345 4.315803 CGTCCCAAATAAGTGACTCAACT 58.684 43.478 0.00 0.00 0.00 3.16
3126 3346 3.435671 CCGTCCCAAATAAGTGACTCAAC 59.564 47.826 0.00 0.00 0.00 3.18
3127 3347 3.325425 TCCGTCCCAAATAAGTGACTCAA 59.675 43.478 0.00 0.00 0.00 3.02
3128 3348 2.901192 TCCGTCCCAAATAAGTGACTCA 59.099 45.455 0.00 0.00 0.00 3.41
3129 3349 3.522553 CTCCGTCCCAAATAAGTGACTC 58.477 50.000 0.00 0.00 0.00 3.36
3130 3350 2.236395 CCTCCGTCCCAAATAAGTGACT 59.764 50.000 0.00 0.00 0.00 3.41
3132 3352 1.557832 CCCTCCGTCCCAAATAAGTGA 59.442 52.381 0.00 0.00 0.00 3.41
3133 3353 1.557832 TCCCTCCGTCCCAAATAAGTG 59.442 52.381 0.00 0.00 0.00 3.16
3135 3355 1.838077 ACTCCCTCCGTCCCAAATAAG 59.162 52.381 0.00 0.00 0.00 1.73
3136 3356 1.961133 ACTCCCTCCGTCCCAAATAA 58.039 50.000 0.00 0.00 0.00 1.40
3137 3357 2.245546 TCTACTCCCTCCGTCCCAAATA 59.754 50.000 0.00 0.00 0.00 1.40
3138 3358 1.007963 TCTACTCCCTCCGTCCCAAAT 59.992 52.381 0.00 0.00 0.00 2.32
3139 3359 0.410663 TCTACTCCCTCCGTCCCAAA 59.589 55.000 0.00 0.00 0.00 3.28
3406 3635 1.228552 TCTGAAAAGTGGGGGCAGC 60.229 57.895 0.00 0.00 0.00 5.25
3753 3993 0.952497 ACGACGCGTCTTAGACAGGA 60.952 55.000 33.94 0.00 33.69 3.86
3795 4035 8.621532 AAAATAAGAGTAGCACAAATGTCAGA 57.378 30.769 0.00 0.00 0.00 3.27
3998 4238 7.861372 ACGGTTATCTGAAATGATTAGTAGTCG 59.139 37.037 0.00 0.00 0.00 4.18
4068 4504 2.019249 CATGGATGGAACTGCGTTCAT 58.981 47.619 18.49 11.97 43.54 2.57
4131 4575 8.960591 GTTCATGCTATAGGTATAATTTGGCAT 58.039 33.333 1.04 0.00 38.22 4.40
4156 4600 4.412528 AGGGAAGTTACTTTCTGAACTGGT 59.587 41.667 3.17 0.00 36.05 4.00
4339 4783 4.565166 GGGCACAAACTTTCAACTACAAAC 59.435 41.667 0.00 0.00 0.00 2.93
4352 4796 1.212935 AGTTCAGTCAGGGCACAAACT 59.787 47.619 0.00 0.00 0.00 2.66
4358 4802 0.535780 CTGCAAGTTCAGTCAGGGCA 60.536 55.000 0.00 0.00 0.00 5.36
4387 4831 3.074687 TGGGGGAGCATTTGTAAGTTGTA 59.925 43.478 0.00 0.00 0.00 2.41
4634 5095 9.625747 ATGCCCCCAAAATTTAAAATATAGTTG 57.374 29.630 0.00 0.00 0.00 3.16
4666 5129 9.823647 GAATAGGACTTACATTTTGAGATGAGA 57.176 33.333 0.00 0.00 0.00 3.27
4907 5388 0.234365 TAACCGTTAACGTTTGCGCC 59.766 50.000 25.15 0.00 42.83 6.53
4908 5389 1.899971 CATAACCGTTAACGTTTGCGC 59.100 47.619 25.15 0.00 42.83 6.09
4909 5390 2.497915 CCATAACCGTTAACGTTTGCG 58.502 47.619 25.15 11.54 44.93 4.85
4911 5392 3.186817 TCTGCCATAACCGTTAACGTTTG 59.813 43.478 25.15 15.84 37.74 2.93
4912 5393 3.401182 TCTGCCATAACCGTTAACGTTT 58.599 40.909 25.15 20.25 37.74 3.60
4913 5394 2.997986 CTCTGCCATAACCGTTAACGTT 59.002 45.455 25.15 20.01 37.74 3.99
4914 5395 2.028748 ACTCTGCCATAACCGTTAACGT 60.029 45.455 25.15 11.45 37.74 3.99
4915 5396 2.613691 ACTCTGCCATAACCGTTAACG 58.386 47.619 20.99 20.99 39.44 3.18
4916 5397 5.870978 TCTAAACTCTGCCATAACCGTTAAC 59.129 40.000 0.00 0.00 0.00 2.01
4917 5398 6.040209 TCTAAACTCTGCCATAACCGTTAA 57.960 37.500 0.00 0.00 0.00 2.01
4918 5399 5.664294 TCTAAACTCTGCCATAACCGTTA 57.336 39.130 0.00 0.00 0.00 3.18
4919 5400 4.546829 TCTAAACTCTGCCATAACCGTT 57.453 40.909 0.00 0.00 0.00 4.44
4920 5401 4.546829 TTCTAAACTCTGCCATAACCGT 57.453 40.909 0.00 0.00 0.00 4.83
4921 5402 5.642063 TCTTTTCTAAACTCTGCCATAACCG 59.358 40.000 0.00 0.00 0.00 4.44
4922 5403 7.631717 ATCTTTTCTAAACTCTGCCATAACC 57.368 36.000 0.00 0.00 0.00 2.85
4923 5404 8.730680 TGAATCTTTTCTAAACTCTGCCATAAC 58.269 33.333 0.00 0.00 32.78 1.89
4924 5405 8.862325 TGAATCTTTTCTAAACTCTGCCATAA 57.138 30.769 0.00 0.00 32.78 1.90
4925 5406 8.103305 ACTGAATCTTTTCTAAACTCTGCCATA 58.897 33.333 0.00 0.00 32.78 2.74
4926 5407 6.944862 ACTGAATCTTTTCTAAACTCTGCCAT 59.055 34.615 0.00 0.00 32.78 4.40
4927 5408 6.205464 CACTGAATCTTTTCTAAACTCTGCCA 59.795 38.462 0.00 0.00 32.78 4.92
4928 5409 6.428159 TCACTGAATCTTTTCTAAACTCTGCC 59.572 38.462 0.00 0.00 32.78 4.85
4929 5410 7.426929 TCACTGAATCTTTTCTAAACTCTGC 57.573 36.000 0.00 0.00 32.78 4.26
4936 5417 9.784531 ACTGAAGAATCACTGAATCTTTTCTAA 57.215 29.630 10.16 0.00 32.71 2.10
4937 5418 9.784531 AACTGAAGAATCACTGAATCTTTTCTA 57.215 29.630 10.16 0.00 32.71 2.10
4938 5419 8.566260 CAACTGAAGAATCACTGAATCTTTTCT 58.434 33.333 10.16 0.00 32.71 2.52
4939 5420 8.562892 TCAACTGAAGAATCACTGAATCTTTTC 58.437 33.333 10.16 1.02 32.71 2.29
4940 5421 8.455903 TCAACTGAAGAATCACTGAATCTTTT 57.544 30.769 10.16 0.08 32.71 2.27
4941 5422 7.935755 TCTCAACTGAAGAATCACTGAATCTTT 59.064 33.333 10.16 0.00 32.71 2.52
4942 5423 7.448420 TCTCAACTGAAGAATCACTGAATCTT 58.552 34.615 8.81 8.81 34.90 2.40
4943 5424 7.002250 TCTCAACTGAAGAATCACTGAATCT 57.998 36.000 0.00 0.00 0.00 2.40
4944 5425 7.664082 TTCTCAACTGAAGAATCACTGAATC 57.336 36.000 0.00 0.00 0.00 2.52
4945 5426 8.455903 TTTTCTCAACTGAAGAATCACTGAAT 57.544 30.769 0.00 0.00 0.00 2.57
4946 5427 7.770433 TCTTTTCTCAACTGAAGAATCACTGAA 59.230 33.333 0.00 0.00 0.00 3.02
4947 5428 7.275183 TCTTTTCTCAACTGAAGAATCACTGA 58.725 34.615 0.00 0.00 0.00 3.41
4948 5429 7.488187 TCTTTTCTCAACTGAAGAATCACTG 57.512 36.000 0.00 0.00 0.00 3.66
4949 5430 8.688747 AATCTTTTCTCAACTGAAGAATCACT 57.311 30.769 0.00 0.00 32.47 3.41
4950 5431 8.782144 AGAATCTTTTCTCAACTGAAGAATCAC 58.218 33.333 0.00 0.00 37.69 3.06
4951 5432 8.915057 AGAATCTTTTCTCAACTGAAGAATCA 57.085 30.769 0.00 0.00 37.69 2.57
4952 5433 9.824534 GAAGAATCTTTTCTCAACTGAAGAATC 57.175 33.333 0.00 0.00 41.42 2.52
4953 5434 9.347240 TGAAGAATCTTTTCTCAACTGAAGAAT 57.653 29.630 0.00 0.00 41.42 2.40
4954 5435 8.737168 TGAAGAATCTTTTCTCAACTGAAGAA 57.263 30.769 0.00 0.00 41.42 2.52
4955 5436 8.737168 TTGAAGAATCTTTTCTCAACTGAAGA 57.263 30.769 0.00 0.00 41.42 2.87
4956 5437 9.962783 AATTGAAGAATCTTTTCTCAACTGAAG 57.037 29.630 0.00 0.00 41.42 3.02
4985 5466 9.847706 GACATCATGTATTAGTAGTCGATGAAT 57.152 33.333 0.00 0.00 34.51 2.57
4986 5467 9.067986 AGACATCATGTATTAGTAGTCGATGAA 57.932 33.333 0.00 0.00 34.51 2.57
4987 5468 8.622948 AGACATCATGTATTAGTAGTCGATGA 57.377 34.615 0.00 0.00 34.51 2.92
4988 5469 9.684448 AAAGACATCATGTATTAGTAGTCGATG 57.316 33.333 0.00 0.00 29.51 3.84
4989 5470 9.900710 GAAAGACATCATGTATTAGTAGTCGAT 57.099 33.333 0.00 0.00 29.51 3.59
4990 5471 9.121658 AGAAAGACATCATGTATTAGTAGTCGA 57.878 33.333 0.00 0.00 29.51 4.20
4991 5472 9.737427 AAGAAAGACATCATGTATTAGTAGTCG 57.263 33.333 0.00 0.00 29.51 4.18
4993 5474 9.319143 GCAAGAAAGACATCATGTATTAGTAGT 57.681 33.333 0.00 0.00 29.51 2.73
4994 5475 9.317936 TGCAAGAAAGACATCATGTATTAGTAG 57.682 33.333 0.00 0.00 29.51 2.57
4995 5476 9.665719 TTGCAAGAAAGACATCATGTATTAGTA 57.334 29.630 0.00 0.00 29.51 1.82
4996 5477 8.565896 TTGCAAGAAAGACATCATGTATTAGT 57.434 30.769 0.00 0.00 29.51 2.24
4997 5478 7.642978 GCTTGCAAGAAAGACATCATGTATTAG 59.357 37.037 30.39 0.00 29.51 1.73
4998 5479 7.475015 GCTTGCAAGAAAGACATCATGTATTA 58.525 34.615 30.39 0.00 29.51 0.98
4999 5480 6.327934 GCTTGCAAGAAAGACATCATGTATT 58.672 36.000 30.39 0.00 32.55 1.89
5008 5489 1.100463 TGGCGCTTGCAAGAAAGACA 61.100 50.000 30.39 23.21 41.71 3.41
5029 5510 2.104963 CCCTAAACTCTGCCATACCTCC 59.895 54.545 0.00 0.00 0.00 4.30
5056 5537 1.209127 GTTTGGTGATCCGCGTTGG 59.791 57.895 4.92 0.00 40.09 3.77
5078 5559 3.361158 CGCGGACATTTGGTGCCA 61.361 61.111 0.00 0.00 33.68 4.92
5093 5574 1.278637 CACGTCCAAAAGTGTCCGC 59.721 57.895 0.00 0.00 33.97 5.54
5137 5618 1.915489 TGGTGCCTACAGTTGGATGAT 59.085 47.619 5.05 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.