Multiple sequence alignment - TraesCS1A01G176700

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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 TraesCS1A01G176700 chr1A 100.000 5271 0 0 1 5271 317810200 317815470 0.000000e+00 9734
1 TraesCS1A01G176700 chr1A 98.519 135 2 0 43 177 185844843 185844709 6.820000e-59 239
2 TraesCS1A01G176700 chr1A 98.507 134 2 0 43 176 129388724 129388591 2.450000e-58 237
3 TraesCS1A01G176700 chr1A 99.237 131 1 0 43 173 465306965 465307095 2.450000e-58 237
4 TraesCS1A01G176700 chr1D 95.021 5162 123 39 179 5271 231468049 231462953 0.000000e+00 7986
5 TraesCS1A01G176700 chr1B 95.123 4839 126 35 479 5271 365018801 365023575 0.000000e+00 7528
6 TraesCS1A01G176700 chr1B 89.441 322 16 12 179 488 366295499 366295184 1.780000e-104 390
7 TraesCS1A01G176700 chr5A 87.541 305 31 6 3185 3487 708807355 708807056 3.910000e-91 346
8 TraesCS1A01G176700 chr5A 98.519 135 2 0 39 173 122639090 122639224 6.820000e-59 239
9 TraesCS1A01G176700 chr5A 97.794 136 3 0 41 176 119998456 119998321 8.820000e-58 235
10 TraesCS1A01G176700 chr4B 87.459 303 30 7 3185 3483 671632078 671631780 5.050000e-90 342
11 TraesCS1A01G176700 chrUn 86.581 313 34 7 3185 3493 28396958 28397266 6.540000e-89 339
12 TraesCS1A01G176700 chr2A 87.814 279 34 0 3184 3462 637678932 637678654 1.420000e-85 327
13 TraesCS1A01G176700 chr2A 87.179 156 20 0 2085 2240 637680040 637679885 1.510000e-40 178
14 TraesCS1A01G176700 chr2D 87.097 279 36 0 3184 3462 492509715 492509437 3.060000e-82 316
15 TraesCS1A01G176700 chr2D 85.897 156 22 0 2085 2240 492510808 492510653 3.270000e-37 167
16 TraesCS1A01G176700 chr2B 87.097 279 36 0 3184 3462 578137511 578137233 3.060000e-82 316
17 TraesCS1A01G176700 chr2B 97.810 137 3 0 40 176 374276141 374276005 2.450000e-58 237
18 TraesCS1A01G176700 chr2B 87.179 156 20 0 2085 2240 578138610 578138455 1.510000e-40 178
19 TraesCS1A01G176700 chr6D 86.926 283 32 4 3182 3462 313281967 313281688 3.960000e-81 313
20 TraesCS1A01G176700 chr6D 84.967 153 21 2 2084 2235 313282694 313282543 2.540000e-33 154
21 TraesCS1A01G176700 chr5B 99.265 136 1 0 43 178 375742645 375742510 4.080000e-61 246
22 TraesCS1A01G176700 chr5B 96.528 144 5 0 34 177 646662757 646662900 6.820000e-59 239
23 TraesCS1A01G176700 chr3A 97.778 135 3 0 43 177 90279454 90279588 3.170000e-57 233
24 TraesCS1A01G176700 chr6B 83.333 156 24 2 2081 2235 512872807 512872961 5.500000e-30 143
25 TraesCS1A01G176700 chr6A 83.553 152 25 0 2084 2235 450465984 450465833 5.500000e-30 143


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 TraesCS1A01G176700 chr1A 317810200 317815470 5270 False 9734.0 9734 100.0000 1 5271 1 chr1A.!!$F1 5270
1 TraesCS1A01G176700 chr1D 231462953 231468049 5096 True 7986.0 7986 95.0210 179 5271 1 chr1D.!!$R1 5092
2 TraesCS1A01G176700 chr1B 365018801 365023575 4774 False 7528.0 7528 95.1230 479 5271 1 chr1B.!!$F1 4792
3 TraesCS1A01G176700 chr2A 637678654 637680040 1386 True 252.5 327 87.4965 2085 3462 2 chr2A.!!$R1 1377
4 TraesCS1A01G176700 chr2D 492509437 492510808 1371 True 241.5 316 86.4970 2085 3462 2 chr2D.!!$R1 1377
5 TraesCS1A01G176700 chr2B 578137233 578138610 1377 True 247.0 316 87.1380 2085 3462 2 chr2B.!!$R2 1377
6 TraesCS1A01G176700 chr6D 313281688 313282694 1006 True 233.5 313 85.9465 2084 3462 2 chr6D.!!$R1 1378

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
138 139 0.032813 CACCCTCAATCCCTGCCAAT 60.033 55.000 0.00 0.0 0.00 3.16 F
494 519 0.035881 CCACATCATCCCCCTCATCG 59.964 60.000 0.00 0.0 0.00 3.84 F
1767 1818 0.685097 AGCTGTCTTTTACTCCGGCA 59.315 50.000 0.00 0.0 0.00 5.69 F
1953 2004 1.001048 GCATGCAGCTTTTGTGTGAGA 60.001 47.619 14.21 0.0 41.15 3.27 F
2937 3182 2.100631 CCAGTTCATCCACGACCGC 61.101 63.158 0.00 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1763 1814 1.159285 TGCAGAAATTCAGAGTGCCG 58.841 50.000 0.00 0.0 32.99 5.69 R
2399 2593 1.072331 CTCAAGTTGCCCACTACCACT 59.928 52.381 0.00 0.0 32.94 4.00 R
3149 3403 3.818787 CCACCGGACCCGTCGTAG 61.819 72.222 9.46 0.0 37.81 3.51 R
3898 4266 1.405463 TCCATCGTCGTCTCCTTCATG 59.595 52.381 0.00 0.0 0.00 3.07 R
4592 4973 0.179084 GCCGCTAGCTGGACATGTAA 60.179 55.000 23.94 0.0 38.99 2.41 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
27 28 2.951457 AAAAATGGTTAATCCGGCGG 57.049 45.000 22.51 22.51 39.52 6.13
28 29 2.131776 AAAATGGTTAATCCGGCGGA 57.868 45.000 33.10 33.10 39.52 5.54
29 30 2.358322 AAATGGTTAATCCGGCGGAT 57.642 45.000 34.54 34.54 45.46 4.18
30 31 3.495434 AAATGGTTAATCCGGCGGATA 57.505 42.857 38.90 24.75 42.27 2.59
31 32 3.495434 AATGGTTAATCCGGCGGATAA 57.505 42.857 38.90 27.75 42.27 1.75
32 33 2.243602 TGGTTAATCCGGCGGATAAC 57.756 50.000 38.90 34.05 42.27 1.89
33 34 1.485480 TGGTTAATCCGGCGGATAACA 59.515 47.619 38.90 30.14 42.27 2.41
34 35 2.105134 TGGTTAATCCGGCGGATAACAT 59.895 45.455 38.90 26.26 42.27 2.71
35 36 3.324268 TGGTTAATCCGGCGGATAACATA 59.676 43.478 38.90 25.19 42.27 2.29
36 37 4.020039 TGGTTAATCCGGCGGATAACATAT 60.020 41.667 38.90 25.18 42.27 1.78
37 38 4.331717 GGTTAATCCGGCGGATAACATATG 59.668 45.833 38.90 3.79 42.27 1.78
38 39 3.973206 AATCCGGCGGATAACATATGA 57.027 42.857 38.90 10.71 42.27 2.15
39 40 2.736144 TCCGGCGGATAACATATGAC 57.264 50.000 27.46 0.00 0.00 3.06
40 41 2.244695 TCCGGCGGATAACATATGACT 58.755 47.619 27.46 0.00 0.00 3.41
41 42 3.423749 TCCGGCGGATAACATATGACTA 58.576 45.455 27.46 0.00 0.00 2.59
42 43 3.827876 TCCGGCGGATAACATATGACTAA 59.172 43.478 27.46 0.00 0.00 2.24
43 44 4.082408 TCCGGCGGATAACATATGACTAAG 60.082 45.833 27.46 0.00 0.00 2.18
44 45 4.174009 CGGCGGATAACATATGACTAAGG 58.826 47.826 10.38 0.00 0.00 2.69
45 46 3.933332 GGCGGATAACATATGACTAAGGC 59.067 47.826 10.38 5.91 0.00 4.35
46 47 3.933332 GCGGATAACATATGACTAAGGCC 59.067 47.826 10.38 0.00 0.00 5.19
47 48 4.322801 GCGGATAACATATGACTAAGGCCT 60.323 45.833 10.38 0.00 0.00 5.19
48 49 5.794894 CGGATAACATATGACTAAGGCCTT 58.205 41.667 24.18 24.18 0.00 4.35
49 50 5.639506 CGGATAACATATGACTAAGGCCTTG 59.360 44.000 28.77 19.17 0.00 3.61
50 51 6.534634 GGATAACATATGACTAAGGCCTTGT 58.465 40.000 28.77 22.17 0.00 3.16
51 52 6.998673 GGATAACATATGACTAAGGCCTTGTT 59.001 38.462 28.77 21.95 0.00 2.83
52 53 7.173390 GGATAACATATGACTAAGGCCTTGTTC 59.827 40.741 28.77 22.17 0.00 3.18
53 54 4.442706 ACATATGACTAAGGCCTTGTTCG 58.557 43.478 28.77 15.14 0.00 3.95
54 55 4.081087 ACATATGACTAAGGCCTTGTTCGT 60.081 41.667 28.77 23.88 0.00 3.85
55 56 2.922740 TGACTAAGGCCTTGTTCGTT 57.077 45.000 28.77 1.45 0.00 3.85
56 57 3.202829 TGACTAAGGCCTTGTTCGTTT 57.797 42.857 28.77 0.57 0.00 3.60
57 58 4.339872 TGACTAAGGCCTTGTTCGTTTA 57.660 40.909 28.77 4.02 0.00 2.01
58 59 4.706035 TGACTAAGGCCTTGTTCGTTTAA 58.294 39.130 28.77 3.22 0.00 1.52
59 60 5.310451 TGACTAAGGCCTTGTTCGTTTAAT 58.690 37.500 28.77 0.00 0.00 1.40
60 61 5.410439 TGACTAAGGCCTTGTTCGTTTAATC 59.590 40.000 28.77 5.17 0.00 1.75
61 62 4.698780 ACTAAGGCCTTGTTCGTTTAATCC 59.301 41.667 28.77 0.00 0.00 3.01
62 63 3.434940 AGGCCTTGTTCGTTTAATCCT 57.565 42.857 0.00 0.00 0.00 3.24
63 64 3.344515 AGGCCTTGTTCGTTTAATCCTC 58.655 45.455 0.00 0.00 0.00 3.71
64 65 2.422479 GGCCTTGTTCGTTTAATCCTCC 59.578 50.000 0.00 0.00 0.00 4.30
65 66 3.344515 GCCTTGTTCGTTTAATCCTCCT 58.655 45.455 0.00 0.00 0.00 3.69
66 67 3.374367 GCCTTGTTCGTTTAATCCTCCTC 59.626 47.826 0.00 0.00 0.00 3.71
67 68 3.939592 CCTTGTTCGTTTAATCCTCCTCC 59.060 47.826 0.00 0.00 0.00 4.30
68 69 3.622166 TGTTCGTTTAATCCTCCTCCC 57.378 47.619 0.00 0.00 0.00 4.30
69 70 2.907696 TGTTCGTTTAATCCTCCTCCCA 59.092 45.455 0.00 0.00 0.00 4.37
70 71 3.328343 TGTTCGTTTAATCCTCCTCCCAA 59.672 43.478 0.00 0.00 0.00 4.12
71 72 3.906720 TCGTTTAATCCTCCTCCCAAG 57.093 47.619 0.00 0.00 0.00 3.61
72 73 2.504175 TCGTTTAATCCTCCTCCCAAGG 59.496 50.000 0.00 0.00 44.89 3.61
73 74 2.421529 CGTTTAATCCTCCTCCCAAGGG 60.422 54.545 0.00 0.00 43.56 3.95
74 75 1.907240 TTAATCCTCCTCCCAAGGGG 58.093 55.000 5.08 0.00 43.63 4.79
87 88 2.834638 CAAGGGGATTGGAGTGGATT 57.165 50.000 0.00 0.00 35.08 3.01
88 89 2.381911 CAAGGGGATTGGAGTGGATTG 58.618 52.381 0.00 0.00 35.08 2.67
89 90 0.929244 AGGGGATTGGAGTGGATTGG 59.071 55.000 0.00 0.00 0.00 3.16
90 91 0.926293 GGGGATTGGAGTGGATTGGA 59.074 55.000 0.00 0.00 0.00 3.53
91 92 1.133668 GGGGATTGGAGTGGATTGGAG 60.134 57.143 0.00 0.00 0.00 3.86
92 93 1.846439 GGGATTGGAGTGGATTGGAGA 59.154 52.381 0.00 0.00 0.00 3.71
93 94 2.158696 GGGATTGGAGTGGATTGGAGAG 60.159 54.545 0.00 0.00 0.00 3.20
94 95 2.158696 GGATTGGAGTGGATTGGAGAGG 60.159 54.545 0.00 0.00 0.00 3.69
95 96 2.342406 TTGGAGTGGATTGGAGAGGA 57.658 50.000 0.00 0.00 0.00 3.71
96 97 2.342406 TGGAGTGGATTGGAGAGGAA 57.658 50.000 0.00 0.00 0.00 3.36
97 98 2.850833 TGGAGTGGATTGGAGAGGAAT 58.149 47.619 0.00 0.00 0.00 3.01
98 99 3.192944 TGGAGTGGATTGGAGAGGAATT 58.807 45.455 0.00 0.00 0.00 2.17
99 100 3.593328 TGGAGTGGATTGGAGAGGAATTT 59.407 43.478 0.00 0.00 0.00 1.82
100 101 3.950395 GGAGTGGATTGGAGAGGAATTTG 59.050 47.826 0.00 0.00 0.00 2.32
101 102 3.950395 GAGTGGATTGGAGAGGAATTTGG 59.050 47.826 0.00 0.00 0.00 3.28
102 103 2.428530 GTGGATTGGAGAGGAATTTGGC 59.571 50.000 0.00 0.00 0.00 4.52
103 104 2.312741 TGGATTGGAGAGGAATTTGGCT 59.687 45.455 0.00 0.00 0.00 4.75
104 105 3.245730 TGGATTGGAGAGGAATTTGGCTT 60.246 43.478 0.00 0.00 0.00 4.35
105 106 3.131755 GGATTGGAGAGGAATTTGGCTTG 59.868 47.826 0.00 0.00 0.00 4.01
106 107 2.978156 TGGAGAGGAATTTGGCTTGT 57.022 45.000 0.00 0.00 0.00 3.16
107 108 4.380843 TTGGAGAGGAATTTGGCTTGTA 57.619 40.909 0.00 0.00 0.00 2.41
108 109 3.955471 TGGAGAGGAATTTGGCTTGTAG 58.045 45.455 0.00 0.00 0.00 2.74
109 110 3.282885 GGAGAGGAATTTGGCTTGTAGG 58.717 50.000 0.00 0.00 0.00 3.18
110 111 3.282885 GAGAGGAATTTGGCTTGTAGGG 58.717 50.000 0.00 0.00 0.00 3.53
111 112 2.024941 AGAGGAATTTGGCTTGTAGGGG 60.025 50.000 0.00 0.00 0.00 4.79
112 113 2.000048 AGGAATTTGGCTTGTAGGGGA 59.000 47.619 0.00 0.00 0.00 4.81
113 114 2.587307 AGGAATTTGGCTTGTAGGGGAT 59.413 45.455 0.00 0.00 0.00 3.85
114 115 2.959030 GGAATTTGGCTTGTAGGGGATC 59.041 50.000 0.00 0.00 0.00 3.36
115 116 3.373110 GGAATTTGGCTTGTAGGGGATCT 60.373 47.826 0.00 0.00 0.00 2.75
116 117 4.141251 GGAATTTGGCTTGTAGGGGATCTA 60.141 45.833 0.00 0.00 0.00 1.98
117 118 5.445964 GAATTTGGCTTGTAGGGGATCTAA 58.554 41.667 0.00 0.00 0.00 2.10
118 119 5.669798 ATTTGGCTTGTAGGGGATCTAAT 57.330 39.130 0.00 0.00 0.00 1.73
119 120 4.706842 TTGGCTTGTAGGGGATCTAATC 57.293 45.455 0.00 0.00 0.00 1.75
120 121 3.664320 TGGCTTGTAGGGGATCTAATCA 58.336 45.455 0.00 0.00 0.00 2.57
121 122 3.391296 TGGCTTGTAGGGGATCTAATCAC 59.609 47.826 0.00 0.00 0.00 3.06
130 131 4.293662 GGGATCTAATCACCCTCAATCC 57.706 50.000 0.00 0.00 40.39 3.01
131 132 3.009584 GGGATCTAATCACCCTCAATCCC 59.990 52.174 1.98 1.98 42.89 3.85
132 133 3.913163 GGATCTAATCACCCTCAATCCCT 59.087 47.826 0.00 0.00 0.00 4.20
133 134 4.263243 GGATCTAATCACCCTCAATCCCTG 60.263 50.000 0.00 0.00 0.00 4.45
134 135 2.439507 TCTAATCACCCTCAATCCCTGC 59.560 50.000 0.00 0.00 0.00 4.85
135 136 0.259938 AATCACCCTCAATCCCTGCC 59.740 55.000 0.00 0.00 0.00 4.85
136 137 0.920763 ATCACCCTCAATCCCTGCCA 60.921 55.000 0.00 0.00 0.00 4.92
137 138 1.139498 TCACCCTCAATCCCTGCCAA 61.139 55.000 0.00 0.00 0.00 4.52
138 139 0.032813 CACCCTCAATCCCTGCCAAT 60.033 55.000 0.00 0.00 0.00 3.16
139 140 0.259938 ACCCTCAATCCCTGCCAATC 59.740 55.000 0.00 0.00 0.00 2.67
140 141 0.468771 CCCTCAATCCCTGCCAATCC 60.469 60.000 0.00 0.00 0.00 3.01
141 142 0.468771 CCTCAATCCCTGCCAATCCC 60.469 60.000 0.00 0.00 0.00 3.85
142 143 0.468771 CTCAATCCCTGCCAATCCCC 60.469 60.000 0.00 0.00 0.00 4.81
143 144 1.458209 CAATCCCTGCCAATCCCCC 60.458 63.158 0.00 0.00 0.00 5.40
144 145 1.626826 AATCCCTGCCAATCCCCCT 60.627 57.895 0.00 0.00 0.00 4.79
145 146 1.659035 AATCCCTGCCAATCCCCCTC 61.659 60.000 0.00 0.00 0.00 4.30
146 147 2.881491 ATCCCTGCCAATCCCCCTCA 62.881 60.000 0.00 0.00 0.00 3.86
147 148 2.276740 CCTGCCAATCCCCCTCAC 59.723 66.667 0.00 0.00 0.00 3.51
148 149 2.615465 CCTGCCAATCCCCCTCACA 61.615 63.158 0.00 0.00 0.00 3.58
149 150 1.383799 CTGCCAATCCCCCTCACAA 59.616 57.895 0.00 0.00 0.00 3.33
150 151 0.251742 CTGCCAATCCCCCTCACAAA 60.252 55.000 0.00 0.00 0.00 2.83
151 152 0.541764 TGCCAATCCCCCTCACAAAC 60.542 55.000 0.00 0.00 0.00 2.93
152 153 1.257750 GCCAATCCCCCTCACAAACC 61.258 60.000 0.00 0.00 0.00 3.27
153 154 0.114168 CCAATCCCCCTCACAAACCA 59.886 55.000 0.00 0.00 0.00 3.67
154 155 1.256812 CAATCCCCCTCACAAACCAC 58.743 55.000 0.00 0.00 0.00 4.16
155 156 0.114364 AATCCCCCTCACAAACCACC 59.886 55.000 0.00 0.00 0.00 4.61
156 157 0.776080 ATCCCCCTCACAAACCACCT 60.776 55.000 0.00 0.00 0.00 4.00
157 158 1.074951 CCCCCTCACAAACCACCTC 59.925 63.158 0.00 0.00 0.00 3.85
158 159 1.715019 CCCCCTCACAAACCACCTCA 61.715 60.000 0.00 0.00 0.00 3.86
159 160 0.184933 CCCCTCACAAACCACCTCAA 59.815 55.000 0.00 0.00 0.00 3.02
160 161 1.318576 CCCTCACAAACCACCTCAAC 58.681 55.000 0.00 0.00 0.00 3.18
161 162 1.318576 CCTCACAAACCACCTCAACC 58.681 55.000 0.00 0.00 0.00 3.77
162 163 0.944386 CTCACAAACCACCTCAACCG 59.056 55.000 0.00 0.00 0.00 4.44
163 164 0.542333 TCACAAACCACCTCAACCGA 59.458 50.000 0.00 0.00 0.00 4.69
164 165 1.065345 TCACAAACCACCTCAACCGAA 60.065 47.619 0.00 0.00 0.00 4.30
165 166 1.064952 CACAAACCACCTCAACCGAAC 59.935 52.381 0.00 0.00 0.00 3.95
166 167 1.340211 ACAAACCACCTCAACCGAACA 60.340 47.619 0.00 0.00 0.00 3.18
167 168 1.746220 CAAACCACCTCAACCGAACAA 59.254 47.619 0.00 0.00 0.00 2.83
168 169 1.675552 AACCACCTCAACCGAACAAG 58.324 50.000 0.00 0.00 0.00 3.16
169 170 0.179029 ACCACCTCAACCGAACAAGG 60.179 55.000 0.00 0.00 34.94 3.61
170 171 1.515521 CCACCTCAACCGAACAAGGC 61.516 60.000 0.00 0.00 31.79 4.35
171 172 1.228154 ACCTCAACCGAACAAGGCC 60.228 57.895 0.00 0.00 31.79 5.19
172 173 1.073199 CCTCAACCGAACAAGGCCT 59.927 57.895 0.00 0.00 33.69 5.19
173 174 1.237285 CCTCAACCGAACAAGGCCTG 61.237 60.000 5.69 2.82 33.69 4.85
174 175 0.250295 CTCAACCGAACAAGGCCTGA 60.250 55.000 5.69 0.00 33.69 3.86
175 176 0.250295 TCAACCGAACAAGGCCTGAG 60.250 55.000 5.69 4.64 33.69 3.35
176 177 1.073199 AACCGAACAAGGCCTGAGG 59.927 57.895 5.69 8.42 33.69 3.86
177 178 1.705997 AACCGAACAAGGCCTGAGGT 61.706 55.000 5.69 9.14 34.18 3.85
205 206 2.452600 TGTATGGGGAAGGGAAATGC 57.547 50.000 0.00 0.00 0.00 3.56
206 207 1.063266 TGTATGGGGAAGGGAAATGCC 60.063 52.381 0.00 0.00 0.00 4.40
214 215 3.117512 GGGAAGGGAAATGCCTAAGATCA 60.118 47.826 0.00 0.00 36.66 2.92
236 237 5.044919 TCACCACAGAATCCAACATATTCCT 60.045 40.000 0.00 0.00 34.50 3.36
247 248 4.338879 CAACATATTCCTCCATGGGGATC 58.661 47.826 15.22 0.00 43.91 3.36
356 364 4.175516 CTGCTCACATGTTTCTCTCTCTC 58.824 47.826 0.00 0.00 0.00 3.20
357 365 3.831333 TGCTCACATGTTTCTCTCTCTCT 59.169 43.478 0.00 0.00 0.00 3.10
358 366 5.012893 TGCTCACATGTTTCTCTCTCTCTA 58.987 41.667 0.00 0.00 0.00 2.43
359 367 5.105957 TGCTCACATGTTTCTCTCTCTCTAC 60.106 44.000 0.00 0.00 0.00 2.59
360 368 5.678616 GCTCACATGTTTCTCTCTCTCTACC 60.679 48.000 0.00 0.00 0.00 3.18
361 369 5.325239 TCACATGTTTCTCTCTCTCTACCA 58.675 41.667 0.00 0.00 0.00 3.25
362 370 5.954752 TCACATGTTTCTCTCTCTCTACCAT 59.045 40.000 0.00 0.00 0.00 3.55
363 371 7.119387 TCACATGTTTCTCTCTCTCTACCATA 58.881 38.462 0.00 0.00 0.00 2.74
364 372 7.067615 TCACATGTTTCTCTCTCTCTACCATAC 59.932 40.741 0.00 0.00 0.00 2.39
365 373 7.068103 CACATGTTTCTCTCTCTCTACCATACT 59.932 40.741 0.00 0.00 0.00 2.12
373 381 6.912426 TCTCTCTCTACCATACTACCATTGT 58.088 40.000 0.00 0.00 0.00 2.71
399 411 1.760480 GCACTCCTCTCCCTCTCCC 60.760 68.421 0.00 0.00 0.00 4.30
430 455 3.245122 TGGGTTTTTAACTAGCAGAGGGG 60.245 47.826 0.00 0.00 0.00 4.79
494 519 0.035881 CCACATCATCCCCCTCATCG 59.964 60.000 0.00 0.00 0.00 3.84
689 724 1.670059 TTTTCCTCTCCCTTCTCCCC 58.330 55.000 0.00 0.00 0.00 4.81
767 805 2.110011 AGAGCTCCTCTATTCCTCCTCC 59.890 54.545 10.93 0.00 39.28 4.30
768 806 2.110011 GAGCTCCTCTATTCCTCCTCCT 59.890 54.545 0.87 0.00 0.00 3.69
769 807 2.110011 AGCTCCTCTATTCCTCCTCCTC 59.890 54.545 0.00 0.00 0.00 3.71
770 808 2.110011 GCTCCTCTATTCCTCCTCCTCT 59.890 54.545 0.00 0.00 0.00 3.69
771 809 3.437931 GCTCCTCTATTCCTCCTCCTCTT 60.438 52.174 0.00 0.00 0.00 2.85
772 810 4.407365 CTCCTCTATTCCTCCTCCTCTTC 58.593 52.174 0.00 0.00 0.00 2.87
773 811 4.058731 TCCTCTATTCCTCCTCCTCTTCT 58.941 47.826 0.00 0.00 0.00 2.85
774 812 4.484270 TCCTCTATTCCTCCTCCTCTTCTT 59.516 45.833 0.00 0.00 0.00 2.52
775 813 4.832823 CCTCTATTCCTCCTCCTCTTCTTC 59.167 50.000 0.00 0.00 0.00 2.87
776 814 5.400189 CCTCTATTCCTCCTCCTCTTCTTCT 60.400 48.000 0.00 0.00 0.00 2.85
777 815 6.098716 TCTATTCCTCCTCCTCTTCTTCTT 57.901 41.667 0.00 0.00 0.00 2.52
778 816 6.133356 TCTATTCCTCCTCCTCTTCTTCTTC 58.867 44.000 0.00 0.00 0.00 2.87
779 817 4.412060 TTCCTCCTCCTCTTCTTCTTCT 57.588 45.455 0.00 0.00 0.00 2.85
780 818 4.412060 TCCTCCTCCTCTTCTTCTTCTT 57.588 45.455 0.00 0.00 0.00 2.52
781 819 4.349365 TCCTCCTCCTCTTCTTCTTCTTC 58.651 47.826 0.00 0.00 0.00 2.87
782 820 4.045334 TCCTCCTCCTCTTCTTCTTCTTCT 59.955 45.833 0.00 0.00 0.00 2.85
783 821 4.777366 CCTCCTCCTCTTCTTCTTCTTCTT 59.223 45.833 0.00 0.00 0.00 2.52
784 822 5.105351 CCTCCTCCTCTTCTTCTTCTTCTTC 60.105 48.000 0.00 0.00 0.00 2.87
785 823 5.650283 TCCTCCTCTTCTTCTTCTTCTTCT 58.350 41.667 0.00 0.00 0.00 2.85
786 824 6.081356 TCCTCCTCTTCTTCTTCTTCTTCTT 58.919 40.000 0.00 0.00 0.00 2.52
787 825 6.210584 TCCTCCTCTTCTTCTTCTTCTTCTTC 59.789 42.308 0.00 0.00 0.00 2.87
788 826 6.211384 CCTCCTCTTCTTCTTCTTCTTCTTCT 59.789 42.308 0.00 0.00 0.00 2.85
789 827 7.256296 CCTCCTCTTCTTCTTCTTCTTCTTCTT 60.256 40.741 0.00 0.00 0.00 2.52
790 828 7.666623 TCCTCTTCTTCTTCTTCTTCTTCTTC 58.333 38.462 0.00 0.00 0.00 2.87
800 838 7.865385 TCTTCTTCTTCTTCTTCTTCTTCTTCG 59.135 37.037 0.00 0.00 0.00 3.79
821 859 1.918293 CCTGACCTGCCTACCACCA 60.918 63.158 0.00 0.00 0.00 4.17
822 860 1.296715 CTGACCTGCCTACCACCAC 59.703 63.158 0.00 0.00 0.00 4.16
823 861 2.185310 CTGACCTGCCTACCACCACC 62.185 65.000 0.00 0.00 0.00 4.61
846 884 5.414144 CCTCATCTCTGTTTCTTTCCCTTTC 59.586 44.000 0.00 0.00 0.00 2.62
868 906 1.106944 CCCGCTCTCCTTCTCTCTCC 61.107 65.000 0.00 0.00 0.00 3.71
908 946 1.186200 GGCCTCCCATCTTTTTCACC 58.814 55.000 0.00 0.00 0.00 4.02
953 991 0.758734 TCACCTCCATTCCCTATGCG 59.241 55.000 0.00 0.00 32.60 4.73
1095 1133 4.514577 CCGCCATTCTCGCCGTCT 62.515 66.667 0.00 0.00 0.00 4.18
1535 1576 1.787847 CGTGCTGTGATTTCCGTCC 59.212 57.895 0.00 0.00 0.00 4.79
1699 1741 2.100584 ACCATCTCTTCGACATGAGAGC 59.899 50.000 14.52 0.00 41.80 4.09
1763 1814 4.249661 CCAGAGAAGCTGTCTTTTACTCC 58.750 47.826 0.00 0.00 43.33 3.85
1767 1818 0.685097 AGCTGTCTTTTACTCCGGCA 59.315 50.000 0.00 0.00 0.00 5.69
1784 1835 2.413765 CGGCACTCTGAATTTCTGCAAG 60.414 50.000 9.66 2.00 0.00 4.01
1926 1977 5.503520 GCCCAAATCGAGTAAAATTCTACCG 60.504 44.000 0.00 0.00 0.00 4.02
1953 2004 1.001048 GCATGCAGCTTTTGTGTGAGA 60.001 47.619 14.21 0.00 41.15 3.27
1991 2043 4.093408 GCATGATGTGTGAGTTCGTATGTT 59.907 41.667 0.00 0.00 0.00 2.71
2937 3182 2.100631 CCAGTTCATCCACGACCGC 61.101 63.158 0.00 0.00 0.00 5.68
3593 3961 2.755876 ATCTCGCAGACGGCTCCA 60.756 61.111 0.00 0.00 41.67 3.86
3729 4097 2.383527 GGCAGCAGGTTCGTCTTCG 61.384 63.158 0.00 0.00 38.55 3.79
3773 4141 4.340263 CGGCGAAAAAGGTAATTAAGCTC 58.660 43.478 0.00 0.00 33.87 4.09
3793 4161 4.035558 GCTCGAAAATATGTGCATTCTGGA 59.964 41.667 0.00 0.00 0.00 3.86
4051 4419 0.739112 ACGAGGACGACTACGAGGAC 60.739 60.000 10.09 0.00 42.66 3.85
4249 4617 2.341101 AACGACGACAGCCGGATCT 61.341 57.895 5.05 0.00 43.93 2.75
4276 4644 1.701847 GGCATGGTCCAGTAGATCCAT 59.298 52.381 0.00 0.00 37.05 3.41
4305 4673 1.134220 CCGGTGACTAGCTCTCTCTCT 60.134 57.143 0.00 0.00 0.00 3.10
4308 4676 2.572290 GTGACTAGCTCTCTCTCTCCC 58.428 57.143 0.00 0.00 0.00 4.30
4309 4677 1.493022 TGACTAGCTCTCTCTCTCCCC 59.507 57.143 0.00 0.00 0.00 4.81
4311 4679 2.108250 GACTAGCTCTCTCTCTCCCCAT 59.892 54.545 0.00 0.00 0.00 4.00
4312 4680 3.329520 GACTAGCTCTCTCTCTCCCCATA 59.670 52.174 0.00 0.00 0.00 2.74
4427 4795 2.167281 CCATATATCTCGGCACCTCCAG 59.833 54.545 0.00 0.00 34.01 3.86
4433 4801 1.379977 TCGGCACCTCCAGACCTAG 60.380 63.158 0.00 0.00 34.01 3.02
4592 4973 3.924922 ACTCCGATATACACCTTCCCTT 58.075 45.455 0.00 0.00 0.00 3.95
4594 4975 5.461327 ACTCCGATATACACCTTCCCTTTA 58.539 41.667 0.00 0.00 0.00 1.85
4602 4983 2.714250 ACACCTTCCCTTTACATGTCCA 59.286 45.455 0.00 0.00 0.00 4.02
4604 4985 2.290960 ACCTTCCCTTTACATGTCCAGC 60.291 50.000 0.00 0.00 0.00 4.85
4606 4987 3.199946 CCTTCCCTTTACATGTCCAGCTA 59.800 47.826 0.00 0.00 0.00 3.32
4607 4988 4.446371 CTTCCCTTTACATGTCCAGCTAG 58.554 47.826 0.00 0.00 0.00 3.42
4608 4989 2.170607 TCCCTTTACATGTCCAGCTAGC 59.829 50.000 6.62 6.62 0.00 3.42
4746 5145 3.198853 AGGGCTTCACTGAGAGGTTAATC 59.801 47.826 0.00 0.00 0.00 1.75
5049 5451 7.435068 AATTGTCCATTATGTATTACCGAGC 57.565 36.000 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.448453 TCCGCCGGATTAACCATTTTT 58.552 42.857 5.05 0.00 38.90 1.94
9 10 2.131776 TCCGCCGGATTAACCATTTT 57.868 45.000 5.05 0.00 38.90 1.82
10 11 2.358322 ATCCGCCGGATTAACCATTT 57.642 45.000 14.09 0.00 39.79 2.32
11 12 3.143728 GTTATCCGCCGGATTAACCATT 58.856 45.455 25.66 0.00 39.79 3.16
12 13 2.105134 TGTTATCCGCCGGATTAACCAT 59.895 45.455 25.66 0.29 39.79 3.55
13 14 1.485480 TGTTATCCGCCGGATTAACCA 59.515 47.619 25.66 12.62 39.79 3.67
14 15 2.243602 TGTTATCCGCCGGATTAACC 57.756 50.000 25.66 10.16 39.79 2.85
15 16 5.063060 GTCATATGTTATCCGCCGGATTAAC 59.937 44.000 25.66 22.87 39.79 2.01
16 17 5.046878 AGTCATATGTTATCCGCCGGATTAA 60.047 40.000 25.66 13.19 39.79 1.40
17 18 4.464951 AGTCATATGTTATCCGCCGGATTA 59.535 41.667 25.66 13.09 39.79 1.75
18 19 3.260884 AGTCATATGTTATCCGCCGGATT 59.739 43.478 25.66 8.74 39.79 3.01
19 20 2.832129 AGTCATATGTTATCCGCCGGAT 59.168 45.455 23.90 23.90 45.40 4.18
20 21 2.244695 AGTCATATGTTATCCGCCGGA 58.755 47.619 8.97 8.97 35.55 5.14
21 22 2.743636 AGTCATATGTTATCCGCCGG 57.256 50.000 0.00 0.00 0.00 6.13
22 23 4.174009 CCTTAGTCATATGTTATCCGCCG 58.826 47.826 1.90 0.00 0.00 6.46
23 24 3.933332 GCCTTAGTCATATGTTATCCGCC 59.067 47.826 1.90 0.00 0.00 6.13
24 25 3.933332 GGCCTTAGTCATATGTTATCCGC 59.067 47.826 1.90 0.00 0.00 5.54
25 26 5.407407 AGGCCTTAGTCATATGTTATCCG 57.593 43.478 0.00 0.00 0.00 4.18
26 27 6.534634 ACAAGGCCTTAGTCATATGTTATCC 58.465 40.000 20.00 0.00 0.00 2.59
27 28 7.095607 CGAACAAGGCCTTAGTCATATGTTATC 60.096 40.741 20.00 4.73 30.58 1.75
28 29 6.706270 CGAACAAGGCCTTAGTCATATGTTAT 59.294 38.462 20.00 0.00 30.58 1.89
29 30 6.046593 CGAACAAGGCCTTAGTCATATGTTA 58.953 40.000 20.00 0.00 30.58 2.41
30 31 4.876107 CGAACAAGGCCTTAGTCATATGTT 59.124 41.667 20.00 16.26 32.89 2.71
31 32 4.081087 ACGAACAAGGCCTTAGTCATATGT 60.081 41.667 20.00 7.22 0.00 2.29
32 33 4.442706 ACGAACAAGGCCTTAGTCATATG 58.557 43.478 20.00 6.46 0.00 1.78
33 34 4.755266 ACGAACAAGGCCTTAGTCATAT 57.245 40.909 20.00 3.82 0.00 1.78
34 35 4.546829 AACGAACAAGGCCTTAGTCATA 57.453 40.909 20.00 0.00 0.00 2.15
35 36 3.418684 AACGAACAAGGCCTTAGTCAT 57.581 42.857 20.00 3.78 0.00 3.06
36 37 2.922740 AACGAACAAGGCCTTAGTCA 57.077 45.000 20.00 0.00 0.00 3.41
37 38 5.163784 GGATTAAACGAACAAGGCCTTAGTC 60.164 44.000 20.00 16.84 0.00 2.59
38 39 4.698780 GGATTAAACGAACAAGGCCTTAGT 59.301 41.667 20.00 15.73 0.00 2.24
39 40 4.941873 AGGATTAAACGAACAAGGCCTTAG 59.058 41.667 20.00 15.05 0.00 2.18
40 41 4.913784 AGGATTAAACGAACAAGGCCTTA 58.086 39.130 20.00 0.00 0.00 2.69
41 42 3.756963 GAGGATTAAACGAACAAGGCCTT 59.243 43.478 13.78 13.78 0.00 4.35
42 43 3.344515 GAGGATTAAACGAACAAGGCCT 58.655 45.455 0.00 0.00 0.00 5.19
43 44 2.422479 GGAGGATTAAACGAACAAGGCC 59.578 50.000 0.00 0.00 0.00 5.19
44 45 3.344515 AGGAGGATTAAACGAACAAGGC 58.655 45.455 0.00 0.00 0.00 4.35
45 46 3.939592 GGAGGAGGATTAAACGAACAAGG 59.060 47.826 0.00 0.00 0.00 3.61
46 47 3.939592 GGGAGGAGGATTAAACGAACAAG 59.060 47.826 0.00 0.00 0.00 3.16
47 48 3.328343 TGGGAGGAGGATTAAACGAACAA 59.672 43.478 0.00 0.00 0.00 2.83
48 49 2.907696 TGGGAGGAGGATTAAACGAACA 59.092 45.455 0.00 0.00 0.00 3.18
49 50 3.622166 TGGGAGGAGGATTAAACGAAC 57.378 47.619 0.00 0.00 0.00 3.95
50 51 3.054655 CCTTGGGAGGAGGATTAAACGAA 60.055 47.826 0.00 0.00 46.74 3.85
51 52 2.504175 CCTTGGGAGGAGGATTAAACGA 59.496 50.000 0.00 0.00 46.74 3.85
52 53 2.421529 CCCTTGGGAGGAGGATTAAACG 60.422 54.545 0.00 0.00 46.74 3.60
53 54 3.298686 CCCTTGGGAGGAGGATTAAAC 57.701 52.381 0.00 0.00 46.74 2.01
68 69 2.381911 CAATCCACTCCAATCCCCTTG 58.618 52.381 0.00 0.00 34.42 3.61
69 70 1.288932 CCAATCCACTCCAATCCCCTT 59.711 52.381 0.00 0.00 0.00 3.95
70 71 0.929244 CCAATCCACTCCAATCCCCT 59.071 55.000 0.00 0.00 0.00 4.79
71 72 0.926293 TCCAATCCACTCCAATCCCC 59.074 55.000 0.00 0.00 0.00 4.81
72 73 1.846439 TCTCCAATCCACTCCAATCCC 59.154 52.381 0.00 0.00 0.00 3.85
73 74 2.158696 CCTCTCCAATCCACTCCAATCC 60.159 54.545 0.00 0.00 0.00 3.01
74 75 2.774234 TCCTCTCCAATCCACTCCAATC 59.226 50.000 0.00 0.00 0.00 2.67
75 76 2.850833 TCCTCTCCAATCCACTCCAAT 58.149 47.619 0.00 0.00 0.00 3.16
76 77 2.342406 TCCTCTCCAATCCACTCCAA 57.658 50.000 0.00 0.00 0.00 3.53
77 78 2.342406 TTCCTCTCCAATCCACTCCA 57.658 50.000 0.00 0.00 0.00 3.86
78 79 3.941704 AATTCCTCTCCAATCCACTCC 57.058 47.619 0.00 0.00 0.00 3.85
79 80 3.950395 CCAAATTCCTCTCCAATCCACTC 59.050 47.826 0.00 0.00 0.00 3.51
80 81 3.879321 GCCAAATTCCTCTCCAATCCACT 60.879 47.826 0.00 0.00 0.00 4.00
81 82 2.428530 GCCAAATTCCTCTCCAATCCAC 59.571 50.000 0.00 0.00 0.00 4.02
82 83 2.312741 AGCCAAATTCCTCTCCAATCCA 59.687 45.455 0.00 0.00 0.00 3.41
83 84 3.023939 AGCCAAATTCCTCTCCAATCC 57.976 47.619 0.00 0.00 0.00 3.01
84 85 3.766051 ACAAGCCAAATTCCTCTCCAATC 59.234 43.478 0.00 0.00 0.00 2.67
85 86 3.782992 ACAAGCCAAATTCCTCTCCAAT 58.217 40.909 0.00 0.00 0.00 3.16
86 87 3.243359 ACAAGCCAAATTCCTCTCCAA 57.757 42.857 0.00 0.00 0.00 3.53
87 88 2.978156 ACAAGCCAAATTCCTCTCCA 57.022 45.000 0.00 0.00 0.00 3.86
88 89 3.282885 CCTACAAGCCAAATTCCTCTCC 58.717 50.000 0.00 0.00 0.00 3.71
89 90 3.282885 CCCTACAAGCCAAATTCCTCTC 58.717 50.000 0.00 0.00 0.00 3.20
90 91 2.024941 CCCCTACAAGCCAAATTCCTCT 60.025 50.000 0.00 0.00 0.00 3.69
91 92 2.025321 TCCCCTACAAGCCAAATTCCTC 60.025 50.000 0.00 0.00 0.00 3.71
92 93 2.000048 TCCCCTACAAGCCAAATTCCT 59.000 47.619 0.00 0.00 0.00 3.36
93 94 2.525105 TCCCCTACAAGCCAAATTCC 57.475 50.000 0.00 0.00 0.00 3.01
94 95 3.903467 AGATCCCCTACAAGCCAAATTC 58.097 45.455 0.00 0.00 0.00 2.17
95 96 5.466127 TTAGATCCCCTACAAGCCAAATT 57.534 39.130 0.00 0.00 0.00 1.82
96 97 5.134339 TGATTAGATCCCCTACAAGCCAAAT 59.866 40.000 0.00 0.00 0.00 2.32
97 98 4.476846 TGATTAGATCCCCTACAAGCCAAA 59.523 41.667 0.00 0.00 0.00 3.28
98 99 4.044308 TGATTAGATCCCCTACAAGCCAA 58.956 43.478 0.00 0.00 0.00 4.52
99 100 3.391296 GTGATTAGATCCCCTACAAGCCA 59.609 47.826 0.00 0.00 0.00 4.75
100 101 3.244596 GGTGATTAGATCCCCTACAAGCC 60.245 52.174 0.00 0.00 0.00 4.35
101 102 3.244596 GGGTGATTAGATCCCCTACAAGC 60.245 52.174 0.00 0.00 37.03 4.01
102 103 4.235372 AGGGTGATTAGATCCCCTACAAG 58.765 47.826 12.50 0.00 43.77 3.16
103 104 4.232091 GAGGGTGATTAGATCCCCTACAA 58.768 47.826 13.56 0.00 44.83 2.41
104 105 3.208922 TGAGGGTGATTAGATCCCCTACA 59.791 47.826 13.56 11.34 44.83 2.74
105 106 3.858135 TGAGGGTGATTAGATCCCCTAC 58.142 50.000 13.56 9.75 44.83 3.18
106 107 4.569676 TTGAGGGTGATTAGATCCCCTA 57.430 45.455 13.56 2.02 44.83 3.53
107 108 3.438131 TTGAGGGTGATTAGATCCCCT 57.562 47.619 13.49 13.49 46.37 4.79
108 109 3.009584 GGATTGAGGGTGATTAGATCCCC 59.990 52.174 0.00 6.44 41.95 4.81
109 110 3.009584 GGGATTGAGGGTGATTAGATCCC 59.990 52.174 3.01 3.01 43.03 3.85
110 111 3.913163 AGGGATTGAGGGTGATTAGATCC 59.087 47.826 0.00 0.00 0.00 3.36
111 112 4.805609 GCAGGGATTGAGGGTGATTAGATC 60.806 50.000 0.00 0.00 0.00 2.75
112 113 3.073650 GCAGGGATTGAGGGTGATTAGAT 59.926 47.826 0.00 0.00 0.00 1.98
113 114 2.439507 GCAGGGATTGAGGGTGATTAGA 59.560 50.000 0.00 0.00 0.00 2.10
114 115 2.487986 GGCAGGGATTGAGGGTGATTAG 60.488 54.545 0.00 0.00 0.00 1.73
115 116 1.494721 GGCAGGGATTGAGGGTGATTA 59.505 52.381 0.00 0.00 0.00 1.75
116 117 0.259938 GGCAGGGATTGAGGGTGATT 59.740 55.000 0.00 0.00 0.00 2.57
117 118 0.920763 TGGCAGGGATTGAGGGTGAT 60.921 55.000 0.00 0.00 0.00 3.06
118 119 1.139498 TTGGCAGGGATTGAGGGTGA 61.139 55.000 0.00 0.00 0.00 4.02
119 120 0.032813 ATTGGCAGGGATTGAGGGTG 60.033 55.000 0.00 0.00 0.00 4.61
120 121 0.259938 GATTGGCAGGGATTGAGGGT 59.740 55.000 0.00 0.00 0.00 4.34
121 122 0.468771 GGATTGGCAGGGATTGAGGG 60.469 60.000 0.00 0.00 0.00 4.30
122 123 0.468771 GGGATTGGCAGGGATTGAGG 60.469 60.000 0.00 0.00 0.00 3.86
123 124 0.468771 GGGGATTGGCAGGGATTGAG 60.469 60.000 0.00 0.00 0.00 3.02
124 125 1.620259 GGGGATTGGCAGGGATTGA 59.380 57.895 0.00 0.00 0.00 2.57
125 126 1.458209 GGGGGATTGGCAGGGATTG 60.458 63.158 0.00 0.00 0.00 2.67
126 127 1.626826 AGGGGGATTGGCAGGGATT 60.627 57.895 0.00 0.00 0.00 3.01
127 128 2.046855 AGGGGGATTGGCAGGGAT 59.953 61.111 0.00 0.00 0.00 3.85
128 129 2.696125 GAGGGGGATTGGCAGGGA 60.696 66.667 0.00 0.00 0.00 4.20
129 130 3.023116 TGAGGGGGATTGGCAGGG 61.023 66.667 0.00 0.00 0.00 4.45
130 131 2.153898 TTGTGAGGGGGATTGGCAGG 62.154 60.000 0.00 0.00 0.00 4.85
131 132 0.251742 TTTGTGAGGGGGATTGGCAG 60.252 55.000 0.00 0.00 0.00 4.85
132 133 0.541764 GTTTGTGAGGGGGATTGGCA 60.542 55.000 0.00 0.00 0.00 4.92
133 134 1.257750 GGTTTGTGAGGGGGATTGGC 61.258 60.000 0.00 0.00 0.00 4.52
134 135 0.114168 TGGTTTGTGAGGGGGATTGG 59.886 55.000 0.00 0.00 0.00 3.16
135 136 1.256812 GTGGTTTGTGAGGGGGATTG 58.743 55.000 0.00 0.00 0.00 2.67
136 137 0.114364 GGTGGTTTGTGAGGGGGATT 59.886 55.000 0.00 0.00 0.00 3.01
137 138 0.776080 AGGTGGTTTGTGAGGGGGAT 60.776 55.000 0.00 0.00 0.00 3.85
138 139 1.386772 AGGTGGTTTGTGAGGGGGA 60.387 57.895 0.00 0.00 0.00 4.81
139 140 1.074951 GAGGTGGTTTGTGAGGGGG 59.925 63.158 0.00 0.00 0.00 5.40
140 141 0.184933 TTGAGGTGGTTTGTGAGGGG 59.815 55.000 0.00 0.00 0.00 4.79
141 142 1.318576 GTTGAGGTGGTTTGTGAGGG 58.681 55.000 0.00 0.00 0.00 4.30
142 143 1.318576 GGTTGAGGTGGTTTGTGAGG 58.681 55.000 0.00 0.00 0.00 3.86
143 144 0.944386 CGGTTGAGGTGGTTTGTGAG 59.056 55.000 0.00 0.00 0.00 3.51
144 145 0.542333 TCGGTTGAGGTGGTTTGTGA 59.458 50.000 0.00 0.00 0.00 3.58
145 146 1.064952 GTTCGGTTGAGGTGGTTTGTG 59.935 52.381 0.00 0.00 0.00 3.33
146 147 1.340211 TGTTCGGTTGAGGTGGTTTGT 60.340 47.619 0.00 0.00 0.00 2.83
147 148 1.384525 TGTTCGGTTGAGGTGGTTTG 58.615 50.000 0.00 0.00 0.00 2.93
148 149 2.021457 CTTGTTCGGTTGAGGTGGTTT 58.979 47.619 0.00 0.00 0.00 3.27
149 150 1.675552 CTTGTTCGGTTGAGGTGGTT 58.324 50.000 0.00 0.00 0.00 3.67
150 151 0.179029 CCTTGTTCGGTTGAGGTGGT 60.179 55.000 0.00 0.00 0.00 4.16
151 152 1.515521 GCCTTGTTCGGTTGAGGTGG 61.516 60.000 0.00 0.00 0.00 4.61
152 153 1.515521 GGCCTTGTTCGGTTGAGGTG 61.516 60.000 0.00 0.00 0.00 4.00
153 154 1.228154 GGCCTTGTTCGGTTGAGGT 60.228 57.895 0.00 0.00 0.00 3.85
154 155 1.073199 AGGCCTTGTTCGGTTGAGG 59.927 57.895 0.00 0.00 0.00 3.86
155 156 0.250295 TCAGGCCTTGTTCGGTTGAG 60.250 55.000 0.00 0.00 0.00 3.02
156 157 0.250295 CTCAGGCCTTGTTCGGTTGA 60.250 55.000 0.00 0.00 0.00 3.18
157 158 1.237285 CCTCAGGCCTTGTTCGGTTG 61.237 60.000 0.00 0.00 0.00 3.77
158 159 1.073199 CCTCAGGCCTTGTTCGGTT 59.927 57.895 0.00 0.00 0.00 4.44
159 160 0.834687 TACCTCAGGCCTTGTTCGGT 60.835 55.000 0.00 8.00 0.00 4.69
160 161 0.108138 CTACCTCAGGCCTTGTTCGG 60.108 60.000 0.00 1.25 0.00 4.30
161 162 0.895530 TCTACCTCAGGCCTTGTTCG 59.104 55.000 0.00 0.00 0.00 3.95
162 163 4.965200 ATATCTACCTCAGGCCTTGTTC 57.035 45.455 0.00 0.00 0.00 3.18
163 164 6.330250 ACAATATATCTACCTCAGGCCTTGTT 59.670 38.462 0.00 0.00 0.00 2.83
164 165 5.846714 ACAATATATCTACCTCAGGCCTTGT 59.153 40.000 0.00 3.09 0.00 3.16
165 166 6.365970 ACAATATATCTACCTCAGGCCTTG 57.634 41.667 0.00 0.00 0.00 3.61
166 167 7.126421 CCATACAATATATCTACCTCAGGCCTT 59.874 40.741 0.00 0.00 0.00 4.35
167 168 6.613271 CCATACAATATATCTACCTCAGGCCT 59.387 42.308 0.00 0.00 0.00 5.19
168 169 6.183361 CCCATACAATATATCTACCTCAGGCC 60.183 46.154 0.00 0.00 0.00 5.19
169 170 6.183361 CCCCATACAATATATCTACCTCAGGC 60.183 46.154 0.00 0.00 0.00 4.85
170 171 7.132805 TCCCCATACAATATATCTACCTCAGG 58.867 42.308 0.00 0.00 0.00 3.86
171 172 8.609617 TTCCCCATACAATATATCTACCTCAG 57.390 38.462 0.00 0.00 0.00 3.35
172 173 7.623677 CCTTCCCCATACAATATATCTACCTCA 59.376 40.741 0.00 0.00 0.00 3.86
173 174 7.071321 CCCTTCCCCATACAATATATCTACCTC 59.929 44.444 0.00 0.00 0.00 3.85
174 175 6.909158 CCCTTCCCCATACAATATATCTACCT 59.091 42.308 0.00 0.00 0.00 3.08
175 176 6.906901 TCCCTTCCCCATACAATATATCTACC 59.093 42.308 0.00 0.00 0.00 3.18
176 177 7.989947 TCCCTTCCCCATACAATATATCTAC 57.010 40.000 0.00 0.00 0.00 2.59
177 178 8.998957 TTTCCCTTCCCCATACAATATATCTA 57.001 34.615 0.00 0.00 0.00 1.98
205 206 4.760530 TGGATTCTGTGGTGATCTTAGG 57.239 45.455 0.00 0.00 0.00 2.69
206 207 5.491070 TGTTGGATTCTGTGGTGATCTTAG 58.509 41.667 0.00 0.00 0.00 2.18
214 215 5.440610 GAGGAATATGTTGGATTCTGTGGT 58.559 41.667 0.00 0.00 34.36 4.16
247 248 3.094572 TCTACAAAACTCCCCTACCTCG 58.905 50.000 0.00 0.00 0.00 4.63
313 314 2.755891 GCATGGAGAGAGAGAGATGGGA 60.756 54.545 0.00 0.00 0.00 4.37
323 324 0.535797 TGTGAGCAGCATGGAGAGAG 59.464 55.000 0.00 0.00 35.86 3.20
356 364 3.554337 GCCGGACAATGGTAGTATGGTAG 60.554 52.174 5.05 0.00 0.00 3.18
357 365 2.366266 GCCGGACAATGGTAGTATGGTA 59.634 50.000 5.05 0.00 0.00 3.25
358 366 1.140252 GCCGGACAATGGTAGTATGGT 59.860 52.381 5.05 0.00 0.00 3.55
359 367 1.140052 TGCCGGACAATGGTAGTATGG 59.860 52.381 5.05 0.00 0.00 2.74
360 368 2.483876 CTGCCGGACAATGGTAGTATG 58.516 52.381 5.05 0.00 34.84 2.39
361 369 1.416401 CCTGCCGGACAATGGTAGTAT 59.584 52.381 5.05 0.00 37.50 2.12
362 370 0.828022 CCTGCCGGACAATGGTAGTA 59.172 55.000 5.05 0.00 37.50 1.82
363 371 1.602237 CCTGCCGGACAATGGTAGT 59.398 57.895 5.05 0.00 37.50 2.73
364 372 1.819632 GCCTGCCGGACAATGGTAG 60.820 63.158 5.05 0.00 38.76 3.18
365 373 2.270850 GCCTGCCGGACAATGGTA 59.729 61.111 5.05 0.00 0.00 3.25
494 519 1.129624 TGTTTGTTGTGTGCAGACGAC 59.870 47.619 24.03 24.03 0.00 4.34
573 598 4.604156 TGATAGCTGTGAAGGAGAGAGAA 58.396 43.478 0.00 0.00 0.00 2.87
689 724 1.306482 TGCAAGGGAGAGAGGAGGG 60.306 63.158 0.00 0.00 0.00 4.30
767 805 9.196552 GAAGAAGAAGAAGAAGAAGAAGAAGAG 57.803 37.037 0.00 0.00 0.00 2.85
768 806 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
769 807 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
770 808 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
771 809 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
772 810 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
773 811 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
774 812 7.865385 CGAAGAAGAAGAAGAAGAAGAAGAAGA 59.135 37.037 0.00 0.00 0.00 2.87
775 813 7.651704 ACGAAGAAGAAGAAGAAGAAGAAGAAG 59.348 37.037 0.00 0.00 0.00 2.85
776 814 7.493367 ACGAAGAAGAAGAAGAAGAAGAAGAA 58.507 34.615 0.00 0.00 0.00 2.52
777 815 7.045126 ACGAAGAAGAAGAAGAAGAAGAAGA 57.955 36.000 0.00 0.00 0.00 2.87
778 816 6.364976 GGACGAAGAAGAAGAAGAAGAAGAAG 59.635 42.308 0.00 0.00 0.00 2.85
779 817 6.217294 GGACGAAGAAGAAGAAGAAGAAGAA 58.783 40.000 0.00 0.00 0.00 2.52
780 818 5.279056 GGGACGAAGAAGAAGAAGAAGAAGA 60.279 44.000 0.00 0.00 0.00 2.87
781 819 4.926832 GGGACGAAGAAGAAGAAGAAGAAG 59.073 45.833 0.00 0.00 0.00 2.85
782 820 4.589374 AGGGACGAAGAAGAAGAAGAAGAA 59.411 41.667 0.00 0.00 0.00 2.52
783 821 4.021894 CAGGGACGAAGAAGAAGAAGAAGA 60.022 45.833 0.00 0.00 0.00 2.87
784 822 4.021894 TCAGGGACGAAGAAGAAGAAGAAG 60.022 45.833 0.00 0.00 0.00 2.85
785 823 3.895656 TCAGGGACGAAGAAGAAGAAGAA 59.104 43.478 0.00 0.00 0.00 2.52
786 824 3.256136 GTCAGGGACGAAGAAGAAGAAGA 59.744 47.826 0.00 0.00 0.00 2.87
787 825 3.580731 GTCAGGGACGAAGAAGAAGAAG 58.419 50.000 0.00 0.00 0.00 2.85
788 826 2.299297 GGTCAGGGACGAAGAAGAAGAA 59.701 50.000 0.00 0.00 32.65 2.52
789 827 1.893801 GGTCAGGGACGAAGAAGAAGA 59.106 52.381 0.00 0.00 32.65 2.87
790 828 1.896465 AGGTCAGGGACGAAGAAGAAG 59.104 52.381 0.00 0.00 32.65 2.85
800 838 1.612442 TGGTAGGCAGGTCAGGGAC 60.612 63.158 0.00 0.00 0.00 4.46
821 859 3.913163 AGGGAAAGAAACAGAGATGAGGT 59.087 43.478 0.00 0.00 0.00 3.85
822 860 4.566426 AGGGAAAGAAACAGAGATGAGG 57.434 45.455 0.00 0.00 0.00 3.86
823 861 5.414144 GGAAAGGGAAAGAAACAGAGATGAG 59.586 44.000 0.00 0.00 0.00 2.90
868 906 1.294659 GGACAGCCAGAAAGAGCACG 61.295 60.000 0.00 0.00 0.00 5.34
908 946 5.279406 GGAATGATCAGTACATGAGAGGGAG 60.279 48.000 0.00 0.00 42.53 4.30
953 991 1.502190 GCAAAGCGTTACCAGAGGC 59.498 57.895 0.00 0.00 0.00 4.70
1018 1056 4.790962 ACCCTGATGCTGCGGCTG 62.791 66.667 20.27 1.15 39.59 4.85
1019 1057 4.790962 CACCCTGATGCTGCGGCT 62.791 66.667 20.27 3.90 39.59 5.52
1221 1262 1.801913 CTCTTCGTCGAAGCCCACG 60.802 63.158 26.65 6.71 39.29 4.94
1461 1502 1.928567 AATTTCCGGCCTCCAGGGA 60.929 57.895 0.00 0.00 37.23 4.20
1521 1562 2.452813 CGGCGGACGGAAATCACAG 61.453 63.158 0.00 0.00 39.42 3.66
1763 1814 1.159285 TGCAGAAATTCAGAGTGCCG 58.841 50.000 0.00 0.00 32.99 5.69
1767 1818 4.924305 TTTGCTTGCAGAAATTCAGAGT 57.076 36.364 0.00 0.00 0.00 3.24
1784 1835 4.152223 CGGGAATCAAAATCCAACTTTTGC 59.848 41.667 4.77 0.00 42.93 3.68
1926 1977 2.264813 CAAAAGCTGCATGCATGTACC 58.735 47.619 26.79 14.77 45.94 3.34
1953 2004 5.001232 ACATCATGCAAGTAAACCGTAACT 58.999 37.500 0.00 0.00 0.00 2.24
1991 2043 1.678627 ACGCTACAACCACAATTGCAA 59.321 42.857 5.05 0.00 32.47 4.08
2399 2593 1.072331 CTCAAGTTGCCCACTACCACT 59.928 52.381 0.00 0.00 32.94 4.00
2501 2701 2.405594 CTCTTCCCTCGCTCGTCG 59.594 66.667 0.00 0.00 40.15 5.12
2937 3182 4.379243 AGGTGGCTGCGAAGACGG 62.379 66.667 0.00 0.00 40.15 4.79
3149 3403 3.818787 CCACCGGACCCGTCGTAG 61.819 72.222 9.46 0.00 37.81 3.51
3773 4141 5.684184 CACATCCAGAATGCACATATTTTCG 59.316 40.000 0.00 0.00 39.12 3.46
3898 4266 1.405463 TCCATCGTCGTCTCCTTCATG 59.595 52.381 0.00 0.00 0.00 3.07
3961 4329 1.438651 GGTTGTAGCTGTTGATCGCA 58.561 50.000 0.00 0.00 0.00 5.10
4051 4419 2.125229 TCGTCCTCCTCGTCCTCG 60.125 66.667 0.00 0.00 38.55 4.63
4249 4617 1.383799 CTGGACCATGCCCAGGAAA 59.616 57.895 19.17 0.00 45.66 3.13
4305 4673 2.178984 GGAATTGATTGGGGTATGGGGA 59.821 50.000 0.00 0.00 0.00 4.81
4308 4676 3.507233 CGATGGAATTGATTGGGGTATGG 59.493 47.826 0.00 0.00 0.00 2.74
4309 4677 3.507233 CCGATGGAATTGATTGGGGTATG 59.493 47.826 0.00 0.00 0.00 2.39
4311 4679 2.512056 ACCGATGGAATTGATTGGGGTA 59.488 45.455 5.62 0.00 0.00 3.69
4312 4680 1.287739 ACCGATGGAATTGATTGGGGT 59.712 47.619 5.62 0.00 0.00 4.95
4592 4973 0.179084 GCCGCTAGCTGGACATGTAA 60.179 55.000 23.94 0.00 38.99 2.41
4594 4975 2.187946 GCCGCTAGCTGGACATGT 59.812 61.111 23.94 0.00 38.99 3.21
4746 5145 1.481871 ACCACCCCGATGTAGTAGTG 58.518 55.000 0.00 0.00 0.00 2.74
5009 5411 6.451393 TGGACAATTTGGGTAATTTCGAAAG 58.549 36.000 16.80 0.53 34.19 2.62
5010 5412 6.406692 TGGACAATTTGGGTAATTTCGAAA 57.593 33.333 13.91 13.91 34.19 3.46
5023 5425 7.803189 GCTCGGTAATACATAATGGACAATTTG 59.197 37.037 0.00 0.00 0.00 2.32
5049 5451 9.639601 AAAAACAGTTGGTAAGAAGAAGAAAAG 57.360 29.630 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.