Multiple sequence alignment - TraesCS1D01G142000

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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 TraesCS1D01G142000 chr1D 100.000 5367 0 0 1 5367 196490045 196484679 0.000000e+00 9912.0
1 TraesCS1D01G142000 chr1B 94.289 2031 79 21 3149 5151 269039093 269041114 0.000000e+00 3073.0
2 TraesCS1D01G142000 chr1B 93.967 1674 51 25 806 2449 269036649 269038302 0.000000e+00 2486.0
3 TraesCS1D01G142000 chr1B 94.118 697 30 4 2489 3175 269038308 269039003 0.000000e+00 1050.0
4 TraesCS1D01G142000 chr1B 91.092 595 21 14 162 737 269035966 269036547 0.000000e+00 776.0
5 TraesCS1D01G142000 chr1A 90.405 1532 52 38 460 1932 245537179 245535684 0.000000e+00 1927.0
6 TraesCS1D01G142000 chr1A 94.705 1171 42 12 3049 4211 245529375 245528217 0.000000e+00 1801.0
7 TraesCS1D01G142000 chr1A 94.918 610 30 1 4527 5136 245527622 245527014 0.000000e+00 953.0
8 TraesCS1D01G142000 chr1A 95.767 567 21 2 2489 3053 245535075 245534510 0.000000e+00 911.0
9 TraesCS1D01G142000 chr1A 95.164 517 19 4 1935 2449 245535593 245535081 0.000000e+00 811.0
10 TraesCS1D01G142000 chr1A 94.294 333 7 3 4197 4528 245528057 245527736 2.890000e-137 499.0
11 TraesCS1D01G142000 chr1A 90.734 259 8 6 168 411 245537433 245537176 1.110000e-86 331.0
12 TraesCS1D01G142000 chr1A 90.367 218 16 5 5152 5367 429980952 429980738 1.140000e-71 281.0
13 TraesCS1D01G142000 chr3D 92.661 218 12 4 5152 5367 482259754 482259539 1.450000e-80 311.0
14 TraesCS1D01G142000 chr3D 91.284 218 17 2 5152 5367 39617961 39618178 4.060000e-76 296.0
15 TraesCS1D01G142000 chr3D 90.826 218 18 2 5152 5367 39619219 39619436 1.890000e-74 291.0
16 TraesCS1D01G142000 chr3D 90.826 218 16 4 5152 5367 39616915 39617130 6.800000e-74 289.0
17 TraesCS1D01G142000 chr6A 91.284 218 15 4 5152 5367 74979165 74978950 1.460000e-75 294.0
18 TraesCS1D01G142000 chr6A 90.367 218 17 4 5152 5367 74978198 74978413 3.160000e-72 283.0
19 TraesCS1D01G142000 chr5D 90.278 216 19 2 5153 5367 190052280 190052494 1.140000e-71 281.0
20 TraesCS1D01G142000 chr5D 100.000 28 0 0 2459 2486 393800006 393800033 1.000000e-02 52.8
21 TraesCS1D01G142000 chr2D 90.000 220 16 5 5151 5367 466813867 466813651 4.090000e-71 279.0
22 TraesCS1D01G142000 chr2D 97.826 46 1 0 2445 2490 17068358 17068403 4.460000e-11 80.5
23 TraesCS1D01G142000 chr2D 95.455 44 2 0 2445 2488 246547668 246547711 2.680000e-08 71.3
24 TraesCS1D01G142000 chr4D 87.200 125 15 1 1029 1152 476865628 476865752 2.020000e-29 141.0
25 TraesCS1D01G142000 chr4D 91.954 87 5 2 2721 2807 476867231 476867315 2.630000e-23 121.0
26 TraesCS1D01G142000 chr4B 86.667 120 16 0 1029 1148 600917282 600917401 3.370000e-27 134.0
27 TraesCS1D01G142000 chr4B 91.954 87 5 2 2721 2807 600918933 600919017 2.630000e-23 121.0
28 TraesCS1D01G142000 chr4A 86.667 120 16 0 1029 1148 683606213 683606332 3.370000e-27 134.0
29 TraesCS1D01G142000 chr4A 90.805 87 6 2 2721 2807 683607829 683607913 1.220000e-21 115.0
30 TraesCS1D01G142000 chr3B 97.674 43 1 0 2446 2488 181678900 181678858 2.070000e-09 75.0
31 TraesCS1D01G142000 chr6B 95.556 45 2 0 2446 2490 716350777 716350733 7.460000e-09 73.1


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 TraesCS1D01G142000 chr1D 196484679 196490045 5366 True 9912.000000 9912 100.000000 1 5367 1 chr1D.!!$R1 5366
1 TraesCS1D01G142000 chr1B 269035966 269041114 5148 False 1846.250000 3073 93.366500 162 5151 4 chr1B.!!$F1 4989
2 TraesCS1D01G142000 chr1A 245527014 245529375 2361 True 1084.333333 1801 94.639000 3049 5136 3 chr1A.!!$R2 2087
3 TraesCS1D01G142000 chr1A 245534510 245537433 2923 True 995.000000 1927 93.017500 168 3053 4 chr1A.!!$R3 2885
4 TraesCS1D01G142000 chr3D 39616915 39619436 2521 False 292.000000 296 90.978667 5152 5367 3 chr3D.!!$F1 215


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
32 33 0.031585 CGGACGGATGCGAAAGGATA 59.968 55.000 15.49 0.00 44.47 2.59 F
133 134 0.037790 AGAAGTCTTCCAGCGAGTGC 60.038 55.000 9.04 0.00 43.24 4.40 F
1844 1986 0.242825 TGGCTCGTACAGTTCGAAGG 59.757 55.000 0.00 0.00 36.89 3.46 F
1888 2030 0.469518 CTACCCCTTAGACCCGGGAG 60.470 65.000 32.02 14.55 43.44 4.30 F
3359 3717 1.484653 TGCTAGTGCATACCGGTCAAT 59.515 47.619 12.40 4.91 45.31 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 2022 1.990060 CCACTGTGATCTCCCGGGT 60.990 63.158 22.86 0.0 0.00 5.28 R
1885 2027 2.939103 GCATAACACCACTGTGATCTCC 59.061 50.000 9.86 0.0 45.76 3.71 R
3635 3994 0.675208 AGCTCTCTCTCTTCGCGACA 60.675 55.000 9.15 0.0 0.00 4.35 R
3763 4122 9.243637 TCAGGAAAAATAACAATTTCTGTTTCG 57.756 29.630 0.00 0.0 46.49 3.46 R
4961 5636 0.250338 GTCAAGTGAACTCCGGGCTT 60.250 55.000 0.00 0.0 0.00 4.35 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 2.577593 GTCCCACTACCTGCGGAC 59.422 66.667 0.00 0.00 34.79 4.79
18 19 3.066190 TCCCACTACCTGCGGACG 61.066 66.667 0.00 0.00 0.00 4.79
19 20 4.143333 CCCACTACCTGCGGACGG 62.143 72.222 0.00 0.00 0.00 4.79
20 21 3.066190 CCACTACCTGCGGACGGA 61.066 66.667 0.00 0.00 0.00 4.69
21 22 2.423898 CCACTACCTGCGGACGGAT 61.424 63.158 0.00 0.00 0.00 4.18
22 23 1.226974 CACTACCTGCGGACGGATG 60.227 63.158 0.00 0.00 0.00 3.51
23 24 2.279517 CTACCTGCGGACGGATGC 60.280 66.667 0.00 0.00 0.00 3.91
24 25 4.201679 TACCTGCGGACGGATGCG 62.202 66.667 4.58 4.58 43.57 4.73
26 27 4.812476 CCTGCGGACGGATGCGAA 62.812 66.667 15.49 0.00 43.37 4.70
27 28 2.813474 CTGCGGACGGATGCGAAA 60.813 61.111 15.49 0.00 43.37 3.46
28 29 2.802667 CTGCGGACGGATGCGAAAG 61.803 63.158 15.49 4.58 43.37 2.62
29 30 3.564027 GCGGACGGATGCGAAAGG 61.564 66.667 15.49 0.27 43.37 3.11
30 31 2.183300 CGGACGGATGCGAAAGGA 59.817 61.111 15.49 0.00 43.37 3.36
32 33 0.031585 CGGACGGATGCGAAAGGATA 59.968 55.000 15.49 0.00 44.47 2.59
33 34 1.336887 CGGACGGATGCGAAAGGATAT 60.337 52.381 15.49 0.00 44.47 1.63
34 35 2.767505 GGACGGATGCGAAAGGATATT 58.232 47.619 15.49 0.00 44.47 1.28
35 36 3.139077 GGACGGATGCGAAAGGATATTT 58.861 45.455 15.49 0.00 44.47 1.40
36 37 3.058914 GGACGGATGCGAAAGGATATTTG 60.059 47.826 15.49 0.00 44.47 2.32
37 38 3.541632 ACGGATGCGAAAGGATATTTGT 58.458 40.909 15.49 0.00 44.47 2.83
38 39 3.312421 ACGGATGCGAAAGGATATTTGTG 59.688 43.478 15.49 0.00 44.47 3.33
39 40 3.559655 CGGATGCGAAAGGATATTTGTGA 59.440 43.478 0.00 0.00 44.47 3.58
40 41 4.319046 CGGATGCGAAAGGATATTTGTGAG 60.319 45.833 0.00 0.00 44.47 3.51
41 42 4.576463 GGATGCGAAAGGATATTTGTGAGT 59.424 41.667 0.00 0.00 44.47 3.41
42 43 5.066505 GGATGCGAAAGGATATTTGTGAGTT 59.933 40.000 0.00 0.00 44.47 3.01
43 44 5.295431 TGCGAAAGGATATTTGTGAGTTG 57.705 39.130 0.00 0.00 0.00 3.16
44 45 4.759693 TGCGAAAGGATATTTGTGAGTTGT 59.240 37.500 0.00 0.00 0.00 3.32
45 46 5.106712 TGCGAAAGGATATTTGTGAGTTGTC 60.107 40.000 0.00 0.00 0.00 3.18
46 47 5.550981 CGAAAGGATATTTGTGAGTTGTCG 58.449 41.667 0.00 0.00 0.00 4.35
47 48 5.120208 CGAAAGGATATTTGTGAGTTGTCGT 59.880 40.000 0.00 0.00 0.00 4.34
48 49 6.347402 CGAAAGGATATTTGTGAGTTGTCGTT 60.347 38.462 0.00 0.00 0.00 3.85
49 50 5.862924 AGGATATTTGTGAGTTGTCGTTG 57.137 39.130 0.00 0.00 0.00 4.10
50 51 4.695455 AGGATATTTGTGAGTTGTCGTTGG 59.305 41.667 0.00 0.00 0.00 3.77
51 52 4.693566 GGATATTTGTGAGTTGTCGTTGGA 59.306 41.667 0.00 0.00 0.00 3.53
52 53 5.163854 GGATATTTGTGAGTTGTCGTTGGAG 60.164 44.000 0.00 0.00 0.00 3.86
53 54 2.971660 TTGTGAGTTGTCGTTGGAGA 57.028 45.000 0.00 0.00 0.00 3.71
54 55 3.469008 TTGTGAGTTGTCGTTGGAGAT 57.531 42.857 0.00 0.00 0.00 2.75
55 56 2.754472 TGTGAGTTGTCGTTGGAGATG 58.246 47.619 0.00 0.00 0.00 2.90
56 57 1.461127 GTGAGTTGTCGTTGGAGATGC 59.539 52.381 0.00 0.00 0.00 3.91
57 58 1.079503 GAGTTGTCGTTGGAGATGCC 58.920 55.000 0.00 0.00 37.10 4.40
58 59 0.687354 AGTTGTCGTTGGAGATGCCT 59.313 50.000 0.00 0.00 37.63 4.75
59 60 1.072331 AGTTGTCGTTGGAGATGCCTT 59.928 47.619 0.00 0.00 37.63 4.35
60 61 2.301870 AGTTGTCGTTGGAGATGCCTTA 59.698 45.455 0.00 0.00 37.63 2.69
61 62 3.055094 AGTTGTCGTTGGAGATGCCTTAT 60.055 43.478 0.00 0.00 37.63 1.73
62 63 2.905075 TGTCGTTGGAGATGCCTTATG 58.095 47.619 0.00 0.00 37.63 1.90
63 64 2.499693 TGTCGTTGGAGATGCCTTATGA 59.500 45.455 0.00 0.00 37.63 2.15
64 65 3.134623 TGTCGTTGGAGATGCCTTATGAT 59.865 43.478 0.00 0.00 37.63 2.45
65 66 4.343814 TGTCGTTGGAGATGCCTTATGATA 59.656 41.667 0.00 0.00 37.63 2.15
66 67 5.163353 TGTCGTTGGAGATGCCTTATGATAA 60.163 40.000 0.00 0.00 37.63 1.75
67 68 5.406780 GTCGTTGGAGATGCCTTATGATAAG 59.593 44.000 5.23 5.23 37.63 1.73
68 69 5.304357 TCGTTGGAGATGCCTTATGATAAGA 59.696 40.000 13.56 0.00 37.63 2.10
69 70 6.014242 TCGTTGGAGATGCCTTATGATAAGAT 60.014 38.462 13.56 0.20 37.63 2.40
70 71 7.178451 TCGTTGGAGATGCCTTATGATAAGATA 59.822 37.037 13.56 2.76 37.63 1.98
71 72 7.984050 CGTTGGAGATGCCTTATGATAAGATAT 59.016 37.037 13.56 7.21 37.63 1.63
86 87 9.624373 ATGATAAGATATAATCCCATTGTCAGC 57.376 33.333 0.00 0.00 0.00 4.26
87 88 7.765819 TGATAAGATATAATCCCATTGTCAGCG 59.234 37.037 0.00 0.00 0.00 5.18
88 89 5.489792 AGATATAATCCCATTGTCAGCGT 57.510 39.130 0.00 0.00 0.00 5.07
89 90 5.240891 AGATATAATCCCATTGTCAGCGTG 58.759 41.667 0.00 0.00 0.00 5.34
90 91 3.558931 ATAATCCCATTGTCAGCGTGA 57.441 42.857 0.00 0.00 0.00 4.35
91 92 2.198827 AATCCCATTGTCAGCGTGAA 57.801 45.000 0.00 0.00 0.00 3.18
92 93 1.453155 ATCCCATTGTCAGCGTGAAC 58.547 50.000 0.00 0.00 0.00 3.18
93 94 0.107643 TCCCATTGTCAGCGTGAACA 59.892 50.000 0.00 0.00 0.00 3.18
94 95 0.950836 CCCATTGTCAGCGTGAACAA 59.049 50.000 2.05 2.05 0.00 2.83
95 96 1.336440 CCCATTGTCAGCGTGAACAAA 59.664 47.619 3.42 0.00 0.00 2.83
96 97 2.223688 CCCATTGTCAGCGTGAACAAAA 60.224 45.455 3.42 0.00 0.00 2.44
97 98 3.443037 CCATTGTCAGCGTGAACAAAAA 58.557 40.909 3.42 0.00 0.00 1.94
98 99 3.242712 CCATTGTCAGCGTGAACAAAAAC 59.757 43.478 3.42 0.00 0.00 2.43
99 100 2.166741 TGTCAGCGTGAACAAAAACG 57.833 45.000 0.00 0.00 42.61 3.60
103 104 3.207877 CGTGAACAAAAACGCGCC 58.792 55.556 5.73 0.00 33.62 6.53
104 105 1.583967 CGTGAACAAAAACGCGCCA 60.584 52.632 5.73 0.00 33.62 5.69
105 106 1.793480 CGTGAACAAAAACGCGCCAC 61.793 55.000 5.73 0.00 33.62 5.01
116 117 3.637714 GCGCCACGAGACAAAAGA 58.362 55.556 0.00 0.00 0.00 2.52
117 118 1.938861 GCGCCACGAGACAAAAGAA 59.061 52.632 0.00 0.00 0.00 2.52
118 119 0.110644 GCGCCACGAGACAAAAGAAG 60.111 55.000 0.00 0.00 0.00 2.85
119 120 1.217882 CGCCACGAGACAAAAGAAGT 58.782 50.000 0.00 0.00 0.00 3.01
120 121 1.192534 CGCCACGAGACAAAAGAAGTC 59.807 52.381 0.00 0.00 36.26 3.01
122 123 2.872858 GCCACGAGACAAAAGAAGTCTT 59.127 45.455 0.00 0.00 45.79 3.01
123 124 3.059529 GCCACGAGACAAAAGAAGTCTTC 60.060 47.826 4.26 4.26 45.79 2.87
124 125 3.495001 CCACGAGACAAAAGAAGTCTTCC 59.505 47.826 9.04 0.00 45.79 3.46
125 126 4.119862 CACGAGACAAAAGAAGTCTTCCA 58.880 43.478 9.04 0.00 45.79 3.53
126 127 4.210120 CACGAGACAAAAGAAGTCTTCCAG 59.790 45.833 9.04 0.03 45.79 3.86
127 128 3.185391 CGAGACAAAAGAAGTCTTCCAGC 59.815 47.826 9.04 0.00 45.79 4.85
128 129 3.134458 AGACAAAAGAAGTCTTCCAGCG 58.866 45.455 9.04 0.00 43.47 5.18
129 130 3.131396 GACAAAAGAAGTCTTCCAGCGA 58.869 45.455 9.04 0.00 34.61 4.93
130 131 3.134458 ACAAAAGAAGTCTTCCAGCGAG 58.866 45.455 9.04 0.00 34.61 5.03
131 132 3.134458 CAAAAGAAGTCTTCCAGCGAGT 58.866 45.455 9.04 0.00 34.61 4.18
132 133 2.447244 AAGAAGTCTTCCAGCGAGTG 57.553 50.000 9.04 0.00 0.00 3.51
133 134 0.037790 AGAAGTCTTCCAGCGAGTGC 60.038 55.000 9.04 0.00 43.24 4.40
134 135 1.004440 AAGTCTTCCAGCGAGTGCC 60.004 57.895 0.00 0.00 44.31 5.01
135 136 2.771763 AAGTCTTCCAGCGAGTGCCG 62.772 60.000 0.00 0.00 44.31 5.69
136 137 3.303135 TCTTCCAGCGAGTGCCGT 61.303 61.111 0.00 0.00 44.31 5.68
137 138 2.357517 CTTCCAGCGAGTGCCGTT 60.358 61.111 0.00 0.00 44.31 4.44
138 139 1.961277 CTTCCAGCGAGTGCCGTTT 60.961 57.895 0.00 0.00 44.31 3.60
139 140 1.901650 CTTCCAGCGAGTGCCGTTTC 61.902 60.000 0.00 0.00 44.31 2.78
140 141 3.777925 CCAGCGAGTGCCGTTTCG 61.778 66.667 0.00 0.00 44.31 3.46
141 142 3.036084 CAGCGAGTGCCGTTTCGT 61.036 61.111 0.00 0.00 44.31 3.85
142 143 3.036084 AGCGAGTGCCGTTTCGTG 61.036 61.111 0.00 0.00 44.31 4.35
143 144 4.719616 GCGAGTGCCGTTTCGTGC 62.720 66.667 0.00 0.00 41.15 5.34
144 145 3.334751 CGAGTGCCGTTTCGTGCA 61.335 61.111 0.00 0.00 32.67 4.57
145 146 2.248431 GAGTGCCGTTTCGTGCAC 59.752 61.111 19.51 19.51 46.21 4.57
147 148 2.351888 GTGCCGTTTCGTGCACAC 60.352 61.111 18.64 6.69 45.66 3.82
148 149 2.820037 TGCCGTTTCGTGCACACA 60.820 55.556 18.64 0.00 30.88 3.72
149 150 2.052237 GCCGTTTCGTGCACACAG 60.052 61.111 18.64 0.04 0.00 3.66
150 151 2.819552 GCCGTTTCGTGCACACAGT 61.820 57.895 18.64 0.00 0.00 3.55
151 152 1.719117 CCGTTTCGTGCACACAGTT 59.281 52.632 18.64 0.00 0.00 3.16
152 153 0.931702 CCGTTTCGTGCACACAGTTA 59.068 50.000 18.64 0.00 0.00 2.24
153 154 1.332552 CCGTTTCGTGCACACAGTTAC 60.333 52.381 18.64 4.72 0.00 2.50
154 155 1.325037 CGTTTCGTGCACACAGTTACA 59.675 47.619 18.64 0.00 0.00 2.41
155 156 2.700694 GTTTCGTGCACACAGTTACAC 58.299 47.619 18.64 0.00 0.00 2.90
160 161 2.969055 GTGCACACAGTTACACGAAAG 58.031 47.619 13.17 0.00 0.00 2.62
161 162 1.937223 TGCACACAGTTACACGAAAGG 59.063 47.619 0.00 0.00 0.00 3.11
162 163 1.333791 GCACACAGTTACACGAAAGGC 60.334 52.381 0.00 0.00 0.00 4.35
163 164 1.937223 CACACAGTTACACGAAAGGCA 59.063 47.619 0.00 0.00 0.00 4.75
164 165 1.937899 ACACAGTTACACGAAAGGCAC 59.062 47.619 0.00 0.00 0.00 5.01
166 167 2.221055 CACAGTTACACGAAAGGCACTC 59.779 50.000 0.00 0.00 38.49 3.51
197 198 6.088824 ACAACCGAAAGATACAAGTACGTAG 58.911 40.000 0.00 0.00 0.00 3.51
215 220 4.049186 CGTAGCCGTAATATCATATGCCC 58.951 47.826 0.00 0.00 0.00 5.36
332 344 0.451135 CACGCAGACAAAAGCTACGC 60.451 55.000 0.00 0.00 0.00 4.42
379 391 2.550487 GGTGTTGCATGACGCCTAA 58.450 52.632 12.89 0.00 44.81 2.69
380 392 0.447801 GGTGTTGCATGACGCCTAAG 59.552 55.000 12.89 0.00 44.81 2.18
384 396 3.001330 GTGTTGCATGACGCCTAAGATAC 59.999 47.826 0.00 0.00 41.33 2.24
385 397 3.118775 TGTTGCATGACGCCTAAGATACT 60.119 43.478 0.00 0.00 41.33 2.12
386 398 3.097877 TGCATGACGCCTAAGATACTG 57.902 47.619 0.00 0.00 41.33 2.74
387 399 1.795286 GCATGACGCCTAAGATACTGC 59.205 52.381 0.00 0.00 32.94 4.40
417 434 0.618680 CTGGTCTGGTCTCCCCATCA 60.619 60.000 0.00 0.00 44.15 3.07
453 470 5.046529 ACACATCCTACTACTCTACGTACG 58.953 45.833 15.01 15.01 0.00 3.67
454 471 5.046529 CACATCCTACTACTCTACGTACGT 58.953 45.833 25.98 25.98 0.00 3.57
455 472 6.183360 ACACATCCTACTACTCTACGTACGTA 60.183 42.308 25.41 25.41 0.00 3.57
456 473 6.143118 CACATCCTACTACTCTACGTACGTAC 59.857 46.154 23.60 15.90 0.00 3.67
947 1030 0.764752 CCTCTAAATCCTCCGCCCCT 60.765 60.000 0.00 0.00 0.00 4.79
963 1046 3.866582 CTCCCCGCCTGACCATCC 61.867 72.222 0.00 0.00 0.00 3.51
1168 1260 3.220110 ACGTCTTCTTAGTCTCACACCA 58.780 45.455 0.00 0.00 0.00 4.17
1298 1406 2.767394 TGGCAGTAGGTAGCGGATTAAA 59.233 45.455 0.00 0.00 0.00 1.52
1378 1486 1.446966 GTCCGAGCTGTTCTCTGCC 60.447 63.158 0.00 0.00 39.70 4.85
1461 1584 5.525199 GAGTTAGTCTCCATGCTAAGTAGC 58.475 45.833 3.26 3.26 41.96 3.58
1602 1726 2.031157 ACAAAACCTGATTGCGCACTAC 60.031 45.455 11.12 5.00 0.00 2.73
1642 1766 7.170658 GTGCTACCTTATTTCTATCTCAAGCAG 59.829 40.741 0.00 0.00 35.92 4.24
1647 1771 6.489361 CCTTATTTCTATCTCAAGCAGCCATT 59.511 38.462 0.00 0.00 0.00 3.16
1712 1837 1.880027 GGAATGGTTCAACTCGCTGTT 59.120 47.619 0.00 0.00 39.92 3.16
1836 1978 3.181475 ACAATATGTCCTGGCTCGTACAG 60.181 47.826 0.00 0.00 35.74 2.74
1844 1986 0.242825 TGGCTCGTACAGTTCGAAGG 59.757 55.000 0.00 0.00 36.89 3.46
1865 2007 8.290325 CGAAGGAAAATAATTATAGCCAACTCC 58.710 37.037 0.00 0.00 0.00 3.85
1880 2022 3.565890 CCAACTCCAGTCTACCCCTTAGA 60.566 52.174 0.00 0.00 34.13 2.10
1888 2030 0.469518 CTACCCCTTAGACCCGGGAG 60.470 65.000 32.02 14.55 43.44 4.30
1911 2053 4.344359 TCACAGTGGTGTTATGCTTGTA 57.656 40.909 0.00 0.00 45.45 2.41
1985 2217 9.955208 TCTATAAATTGCATGCTCTTTTGTATG 57.045 29.630 20.33 11.15 0.00 2.39
1993 2225 8.625786 TGCATGCTCTTTTGTATGATATGTAT 57.374 30.769 20.33 0.00 0.00 2.29
2152 2384 3.927142 CCGACTGTTCAAGTATGGTCTTC 59.073 47.826 0.00 0.00 40.07 2.87
2153 2385 4.322049 CCGACTGTTCAAGTATGGTCTTCT 60.322 45.833 0.00 0.00 40.07 2.85
2260 2492 4.820173 TGGAATTTGCTCATAGAGATGCAG 59.180 41.667 0.00 0.00 33.84 4.41
2296 2528 2.956333 GCCAAAAACTACCAGGAGTTGT 59.044 45.455 0.00 0.00 39.62 3.32
2315 2547 4.948341 TGTTACAAGCACCAACTAGAGA 57.052 40.909 0.00 0.00 0.00 3.10
2433 2665 4.142609 TCTCTGCCATCATTACTTCCAC 57.857 45.455 0.00 0.00 0.00 4.02
2451 2683 7.746703 ACTTCCACCATTTATAAGATACTCCC 58.253 38.462 0.00 0.00 0.00 4.30
2453 2685 7.554959 TCCACCATTTATAAGATACTCCCTC 57.445 40.000 0.00 0.00 0.00 4.30
2454 2686 6.500751 TCCACCATTTATAAGATACTCCCTCC 59.499 42.308 0.00 0.00 0.00 4.30
2455 2687 6.398918 CACCATTTATAAGATACTCCCTCCG 58.601 44.000 0.00 0.00 0.00 4.63
2456 2688 6.014499 CACCATTTATAAGATACTCCCTCCGT 60.014 42.308 0.00 0.00 0.00 4.69
2457 2689 7.177921 CACCATTTATAAGATACTCCCTCCGTA 59.822 40.741 0.00 0.00 0.00 4.02
2458 2690 7.731688 ACCATTTATAAGATACTCCCTCCGTAA 59.268 37.037 0.00 0.00 0.00 3.18
2459 2691 8.591072 CCATTTATAAGATACTCCCTCCGTAAA 58.409 37.037 0.00 0.00 0.00 2.01
2460 2692 9.420551 CATTTATAAGATACTCCCTCCGTAAAC 57.579 37.037 0.00 0.00 0.00 2.01
2461 2693 8.537728 TTTATAAGATACTCCCTCCGTAAACA 57.462 34.615 0.00 0.00 0.00 2.83
2462 2694 8.537728 TTATAAGATACTCCCTCCGTAAACAA 57.462 34.615 0.00 0.00 0.00 2.83
2463 2695 5.750352 AAGATACTCCCTCCGTAAACAAA 57.250 39.130 0.00 0.00 0.00 2.83
2464 2696 5.952347 AGATACTCCCTCCGTAAACAAAT 57.048 39.130 0.00 0.00 0.00 2.32
2465 2697 7.427989 AAGATACTCCCTCCGTAAACAAATA 57.572 36.000 0.00 0.00 0.00 1.40
2466 2698 7.613551 AGATACTCCCTCCGTAAACAAATAT 57.386 36.000 0.00 0.00 0.00 1.28
2467 2699 8.716674 AGATACTCCCTCCGTAAACAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
2468 2700 8.804204 AGATACTCCCTCCGTAAACAAATATAG 58.196 37.037 0.00 0.00 0.00 1.31
2469 2701 6.170846 ACTCCCTCCGTAAACAAATATAGG 57.829 41.667 0.00 0.00 0.00 2.57
2470 2702 5.901276 ACTCCCTCCGTAAACAAATATAGGA 59.099 40.000 0.00 0.00 0.00 2.94
2471 2703 6.041751 ACTCCCTCCGTAAACAAATATAGGAG 59.958 42.308 0.00 0.00 42.36 3.69
2472 2704 4.995487 CCCTCCGTAAACAAATATAGGAGC 59.005 45.833 3.27 0.00 41.62 4.70
2473 2705 4.684703 CCTCCGTAAACAAATATAGGAGCG 59.315 45.833 3.27 0.00 41.62 5.03
2474 2706 5.266733 TCCGTAAACAAATATAGGAGCGT 57.733 39.130 0.00 0.00 0.00 5.07
2475 2707 5.663456 TCCGTAAACAAATATAGGAGCGTT 58.337 37.500 0.00 0.00 0.00 4.84
2476 2708 6.108015 TCCGTAAACAAATATAGGAGCGTTT 58.892 36.000 0.00 0.00 0.00 3.60
2477 2709 7.264221 TCCGTAAACAAATATAGGAGCGTTTA 58.736 34.615 0.00 0.00 0.00 2.01
2478 2710 7.436080 TCCGTAAACAAATATAGGAGCGTTTAG 59.564 37.037 0.00 0.00 31.53 1.85
2479 2711 7.436080 CCGTAAACAAATATAGGAGCGTTTAGA 59.564 37.037 0.00 0.00 31.53 2.10
2480 2712 8.975439 CGTAAACAAATATAGGAGCGTTTAGAT 58.025 33.333 0.00 0.00 31.53 1.98
2482 2714 8.958119 AAACAAATATAGGAGCGTTTAGATCA 57.042 30.769 0.00 0.00 36.90 2.92
2483 2715 7.948278 ACAAATATAGGAGCGTTTAGATCAC 57.052 36.000 0.00 0.00 36.90 3.06
2484 2716 7.727181 ACAAATATAGGAGCGTTTAGATCACT 58.273 34.615 0.00 0.00 36.90 3.41
2485 2717 8.857098 ACAAATATAGGAGCGTTTAGATCACTA 58.143 33.333 0.00 0.00 36.90 2.74
2486 2718 9.692749 CAAATATAGGAGCGTTTAGATCACTAA 57.307 33.333 0.00 0.00 36.90 2.24
2549 2781 3.365472 TCATCTCGATCAGAGGTTCCAA 58.635 45.455 12.54 0.00 46.82 3.53
2621 2853 4.656112 AGAGCTGCACCATATTACCTACTT 59.344 41.667 1.02 0.00 0.00 2.24
2895 3131 4.373156 TCACTCGGAGATCAGATATCCA 57.627 45.455 21.64 9.63 40.68 3.41
3112 3354 3.358111 TGAGAAGTTGGTGACCACAAA 57.642 42.857 2.46 0.00 30.78 2.83
3247 3605 3.526430 CCGCTCTGTAGGCTAGCA 58.474 61.111 18.24 0.00 35.98 3.49
3325 3683 7.121168 TGCCTCATGGTTGTTCTTCTAAATAAG 59.879 37.037 0.00 0.00 35.27 1.73
3333 3691 9.914131 GGTTGTTCTTCTAAATAAGAAAATGCT 57.086 29.630 0.89 0.00 44.75 3.79
3359 3717 1.484653 TGCTAGTGCATACCGGTCAAT 59.515 47.619 12.40 4.91 45.31 2.57
3429 3787 3.436700 GTGAAACTGTGGAACCTTTGG 57.563 47.619 0.00 0.00 34.36 3.28
3821 4184 8.848474 TGTTCCAAACTTGTTATTTTCCAAAA 57.152 26.923 0.00 0.00 0.00 2.44
3903 4266 7.846066 AGTAGACATCAATTCAGTTCTTAGCT 58.154 34.615 0.00 0.00 0.00 3.32
4175 4541 6.633856 AGAACTCAGTTGCATTTTCAGTTTT 58.366 32.000 0.00 0.00 0.00 2.43
4193 4559 5.639082 CAGTTTTGTGGTTGCTTTTTCTTCT 59.361 36.000 0.00 0.00 0.00 2.85
4211 4577 3.682592 TCTAGTAGGCAAGCCCTTAGA 57.317 47.619 7.62 9.62 43.06 2.10
4241 4781 6.150976 TGAATCACAAACAGACTCAGTTTTGT 59.849 34.615 0.93 0.93 37.10 2.83
4369 4909 5.130975 TGGTGGTAGATGCTGTCAATAGATT 59.869 40.000 0.00 0.00 0.00 2.40
4370 4910 5.698545 GGTGGTAGATGCTGTCAATAGATTC 59.301 44.000 0.00 0.00 0.00 2.52
4462 5003 1.717645 GTTGTCGCGTTCTCGTTGTAT 59.282 47.619 5.77 0.00 39.49 2.29
4632 5288 0.388659 TGCGCAAATTGCTTTGTCCT 59.611 45.000 16.42 0.00 43.07 3.85
4635 5291 1.269726 CGCAAATTGCTTTGTCCTGGT 60.270 47.619 16.42 0.00 43.07 4.00
4685 5341 7.649705 TCTTGATTCTTGATGTTAGCGACTATC 59.350 37.037 0.00 0.00 0.00 2.08
4812 5468 1.064906 ACACTCCTGGATGATGCAAGG 60.065 52.381 0.00 0.00 0.00 3.61
4814 5470 0.822532 CTCCTGGATGATGCAAGGCC 60.823 60.000 0.00 0.00 0.00 5.19
4831 5487 2.036256 CAAGGGCCAGGGGAAGTG 59.964 66.667 6.18 0.00 0.00 3.16
4843 5499 0.106967 GGGAAGTGAAGAGGCCATCC 60.107 60.000 5.01 0.00 0.00 3.51
4846 5502 2.637947 GAAGTGAAGAGGCCATCCTTC 58.362 52.381 19.50 19.50 44.46 3.46
4854 5510 2.272146 GCCATCCTTCCCTTCGCA 59.728 61.111 0.00 0.00 0.00 5.10
4921 5596 5.278266 CGTTAGTTTTTCAGGATTCAGCCAA 60.278 40.000 0.00 0.00 0.00 4.52
4961 5636 6.064060 CAGGGGCTATAGATCAATGTTTTCA 58.936 40.000 3.21 0.00 0.00 2.69
4966 5641 6.442112 GCTATAGATCAATGTTTTCAAGCCC 58.558 40.000 3.21 0.00 0.00 5.19
5011 5686 6.917533 AGAAATTGGAAGCATTACTTGACTG 58.082 36.000 0.00 0.00 39.29 3.51
5051 5726 6.636447 CGCAAATTGATATCGGATTTTTGCTA 59.364 34.615 23.20 0.00 43.06 3.49
5055 5730 3.745975 TGATATCGGATTTTTGCTAGGCG 59.254 43.478 0.00 0.00 0.00 5.52
5076 5751 3.745975 CGTCTTTGTTCCACTTATGCTGA 59.254 43.478 0.00 0.00 0.00 4.26
5146 5821 3.366396 TGGGTTCAAGTAAGTGCCAAAA 58.634 40.909 0.00 0.00 0.00 2.44
5175 5850 4.654262 GGAAAGTATCAGGTACTCCCATCA 59.346 45.833 0.00 0.00 42.83 3.07
5199 5874 0.391263 GGTACTCCCGGTGCTTCAAG 60.391 60.000 0.00 0.00 0.00 3.02
5203 5878 1.418637 ACTCCCGGTGCTTCAAGTTTA 59.581 47.619 0.00 0.00 0.00 2.01
5268 5944 5.895636 TGAATGTTCGCAAGGAATGTAAT 57.104 34.783 0.00 0.00 36.92 1.89
5275 5951 6.205853 TGTTCGCAAGGAATGTAATTACAACT 59.794 34.615 21.57 16.27 40.60 3.16
5276 5952 6.811253 TCGCAAGGAATGTAATTACAACTT 57.189 33.333 21.57 20.30 40.60 2.66
5334 8316 8.918658 CATAAGAAACAAACATGTGAAATCTGG 58.081 33.333 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.802667 CTTTCGCATCCGTCCGCAG 61.803 63.158 0.00 0.00 35.54 5.18
11 12 2.813474 CTTTCGCATCCGTCCGCA 60.813 61.111 0.00 0.00 35.54 5.69
12 13 3.564027 CCTTTCGCATCCGTCCGC 61.564 66.667 0.00 0.00 35.54 5.54
13 14 0.031585 TATCCTTTCGCATCCGTCCG 59.968 55.000 0.00 0.00 35.54 4.79
14 15 2.457366 ATATCCTTTCGCATCCGTCC 57.543 50.000 0.00 0.00 35.54 4.79
15 16 3.560068 ACAAATATCCTTTCGCATCCGTC 59.440 43.478 0.00 0.00 35.54 4.79
16 17 3.312421 CACAAATATCCTTTCGCATCCGT 59.688 43.478 0.00 0.00 35.54 4.69
17 18 3.559655 TCACAAATATCCTTTCGCATCCG 59.440 43.478 0.00 0.00 0.00 4.18
18 19 4.576463 ACTCACAAATATCCTTTCGCATCC 59.424 41.667 0.00 0.00 0.00 3.51
19 20 5.741388 ACTCACAAATATCCTTTCGCATC 57.259 39.130 0.00 0.00 0.00 3.91
20 21 5.415701 ACAACTCACAAATATCCTTTCGCAT 59.584 36.000 0.00 0.00 0.00 4.73
21 22 4.759693 ACAACTCACAAATATCCTTTCGCA 59.240 37.500 0.00 0.00 0.00 5.10
22 23 5.296813 ACAACTCACAAATATCCTTTCGC 57.703 39.130 0.00 0.00 0.00 4.70
23 24 5.120208 ACGACAACTCACAAATATCCTTTCG 59.880 40.000 0.00 0.00 0.00 3.46
24 25 6.481954 ACGACAACTCACAAATATCCTTTC 57.518 37.500 0.00 0.00 0.00 2.62
25 26 6.293955 CCAACGACAACTCACAAATATCCTTT 60.294 38.462 0.00 0.00 0.00 3.11
26 27 5.181245 CCAACGACAACTCACAAATATCCTT 59.819 40.000 0.00 0.00 0.00 3.36
27 28 4.695455 CCAACGACAACTCACAAATATCCT 59.305 41.667 0.00 0.00 0.00 3.24
28 29 4.693566 TCCAACGACAACTCACAAATATCC 59.306 41.667 0.00 0.00 0.00 2.59
29 30 5.637810 TCTCCAACGACAACTCACAAATATC 59.362 40.000 0.00 0.00 0.00 1.63
30 31 5.547465 TCTCCAACGACAACTCACAAATAT 58.453 37.500 0.00 0.00 0.00 1.28
31 32 4.951254 TCTCCAACGACAACTCACAAATA 58.049 39.130 0.00 0.00 0.00 1.40
32 33 3.804036 TCTCCAACGACAACTCACAAAT 58.196 40.909 0.00 0.00 0.00 2.32
33 34 3.254470 TCTCCAACGACAACTCACAAA 57.746 42.857 0.00 0.00 0.00 2.83
34 35 2.971660 TCTCCAACGACAACTCACAA 57.028 45.000 0.00 0.00 0.00 3.33
35 36 2.754472 CATCTCCAACGACAACTCACA 58.246 47.619 0.00 0.00 0.00 3.58
36 37 1.461127 GCATCTCCAACGACAACTCAC 59.539 52.381 0.00 0.00 0.00 3.51
37 38 1.608025 GGCATCTCCAACGACAACTCA 60.608 52.381 0.00 0.00 34.01 3.41
38 39 1.079503 GGCATCTCCAACGACAACTC 58.920 55.000 0.00 0.00 34.01 3.01
39 40 0.687354 AGGCATCTCCAACGACAACT 59.313 50.000 0.00 0.00 37.29 3.16
40 41 1.523758 AAGGCATCTCCAACGACAAC 58.476 50.000 0.00 0.00 37.29 3.32
41 42 3.055458 TCATAAGGCATCTCCAACGACAA 60.055 43.478 0.00 0.00 37.29 3.18
42 43 2.499693 TCATAAGGCATCTCCAACGACA 59.500 45.455 0.00 0.00 37.29 4.35
43 44 3.179443 TCATAAGGCATCTCCAACGAC 57.821 47.619 0.00 0.00 37.29 4.34
44 45 5.304357 TCTTATCATAAGGCATCTCCAACGA 59.696 40.000 4.51 0.00 37.29 3.85
45 46 5.541845 TCTTATCATAAGGCATCTCCAACG 58.458 41.667 4.51 0.00 37.29 4.10
60 61 9.624373 GCTGACAATGGGATTATATCTTATCAT 57.376 33.333 0.00 0.00 0.00 2.45
61 62 7.765819 CGCTGACAATGGGATTATATCTTATCA 59.234 37.037 0.00 0.00 0.00 2.15
62 63 7.766278 ACGCTGACAATGGGATTATATCTTATC 59.234 37.037 0.00 0.00 0.00 1.75
63 64 7.550551 CACGCTGACAATGGGATTATATCTTAT 59.449 37.037 0.00 0.00 0.00 1.73
64 65 6.873605 CACGCTGACAATGGGATTATATCTTA 59.126 38.462 0.00 0.00 0.00 2.10
65 66 5.702670 CACGCTGACAATGGGATTATATCTT 59.297 40.000 0.00 0.00 0.00 2.40
66 67 5.012046 TCACGCTGACAATGGGATTATATCT 59.988 40.000 0.00 0.00 0.00 1.98
67 68 5.237815 TCACGCTGACAATGGGATTATATC 58.762 41.667 0.00 0.00 0.00 1.63
68 69 5.227569 TCACGCTGACAATGGGATTATAT 57.772 39.130 0.00 0.00 0.00 0.86
69 70 4.681074 TCACGCTGACAATGGGATTATA 57.319 40.909 0.00 0.00 0.00 0.98
70 71 3.558931 TCACGCTGACAATGGGATTAT 57.441 42.857 0.00 0.00 0.00 1.28
71 72 3.006940 GTTCACGCTGACAATGGGATTA 58.993 45.455 0.00 0.00 0.00 1.75
72 73 1.812571 GTTCACGCTGACAATGGGATT 59.187 47.619 0.00 0.00 0.00 3.01
73 74 1.271325 TGTTCACGCTGACAATGGGAT 60.271 47.619 0.00 0.00 0.00 3.85
74 75 0.107643 TGTTCACGCTGACAATGGGA 59.892 50.000 0.00 0.00 0.00 4.37
75 76 0.950836 TTGTTCACGCTGACAATGGG 59.049 50.000 0.00 0.00 0.00 4.00
76 77 2.772568 TTTGTTCACGCTGACAATGG 57.227 45.000 0.00 0.00 0.00 3.16
77 78 3.061928 CGTTTTTGTTCACGCTGACAATG 60.062 43.478 0.00 0.00 0.00 2.82
78 79 3.105203 CGTTTTTGTTCACGCTGACAAT 58.895 40.909 0.00 0.00 0.00 2.71
79 80 2.510874 CGTTTTTGTTCACGCTGACAA 58.489 42.857 0.00 0.00 0.00 3.18
80 81 2.166741 CGTTTTTGTTCACGCTGACA 57.833 45.000 0.00 0.00 0.00 3.58
86 87 1.583967 TGGCGCGTTTTTGTTCACG 60.584 52.632 8.43 0.00 39.49 4.35
87 88 1.793480 CGTGGCGCGTTTTTGTTCAC 61.793 55.000 13.13 0.00 35.54 3.18
88 89 1.583967 CGTGGCGCGTTTTTGTTCA 60.584 52.632 13.13 0.00 35.54 3.18
89 90 1.259544 CTCGTGGCGCGTTTTTGTTC 61.260 55.000 20.88 0.00 42.13 3.18
90 91 1.298041 CTCGTGGCGCGTTTTTGTT 60.298 52.632 20.88 0.00 42.13 2.83
91 92 2.174969 TCTCGTGGCGCGTTTTTGT 61.175 52.632 20.88 0.00 42.13 2.83
92 93 1.721133 GTCTCGTGGCGCGTTTTTG 60.721 57.895 20.88 7.02 42.13 2.44
93 94 1.707239 TTGTCTCGTGGCGCGTTTTT 61.707 50.000 20.88 0.00 42.13 1.94
94 95 1.707239 TTTGTCTCGTGGCGCGTTTT 61.707 50.000 20.88 0.00 42.13 2.43
95 96 1.707239 TTTTGTCTCGTGGCGCGTTT 61.707 50.000 20.88 0.00 42.13 3.60
96 97 2.101209 CTTTTGTCTCGTGGCGCGTT 62.101 55.000 20.88 0.00 42.13 4.84
97 98 2.586635 TTTTGTCTCGTGGCGCGT 60.587 55.556 20.88 0.00 42.13 6.01
98 99 1.827315 TTCTTTTGTCTCGTGGCGCG 61.827 55.000 15.42 15.42 43.01 6.86
99 100 0.110644 CTTCTTTTGTCTCGTGGCGC 60.111 55.000 0.00 0.00 0.00 6.53
100 101 1.192534 GACTTCTTTTGTCTCGTGGCG 59.807 52.381 0.00 0.00 0.00 5.69
101 102 2.484889 AGACTTCTTTTGTCTCGTGGC 58.515 47.619 0.00 0.00 40.35 5.01
102 103 3.495001 GGAAGACTTCTTTTGTCTCGTGG 59.505 47.826 14.72 0.00 43.16 4.94
103 104 4.119862 TGGAAGACTTCTTTTGTCTCGTG 58.880 43.478 14.72 0.00 43.16 4.35
104 105 4.372656 CTGGAAGACTTCTTTTGTCTCGT 58.627 43.478 14.72 0.00 43.16 4.18
105 106 3.185391 GCTGGAAGACTTCTTTTGTCTCG 59.815 47.826 14.72 0.00 43.16 4.04
106 107 3.185391 CGCTGGAAGACTTCTTTTGTCTC 59.815 47.826 14.72 0.00 43.16 3.36
107 108 3.134458 CGCTGGAAGACTTCTTTTGTCT 58.866 45.455 14.72 0.00 45.55 3.41
108 109 3.131396 TCGCTGGAAGACTTCTTTTGTC 58.869 45.455 14.72 0.00 36.11 3.18
109 110 3.134458 CTCGCTGGAAGACTTCTTTTGT 58.866 45.455 14.72 0.00 36.11 2.83
110 111 3.059325 CACTCGCTGGAAGACTTCTTTTG 60.059 47.826 14.72 3.91 36.11 2.44
111 112 3.134458 CACTCGCTGGAAGACTTCTTTT 58.866 45.455 14.72 0.00 36.11 2.27
112 113 2.760374 CACTCGCTGGAAGACTTCTTT 58.240 47.619 14.72 0.00 36.11 2.52
113 114 1.606737 GCACTCGCTGGAAGACTTCTT 60.607 52.381 14.72 0.00 34.07 2.52
114 115 0.037790 GCACTCGCTGGAAGACTTCT 60.038 55.000 14.72 0.00 34.07 2.85
115 116 1.016653 GGCACTCGCTGGAAGACTTC 61.017 60.000 6.66 6.66 38.60 3.01
116 117 1.004440 GGCACTCGCTGGAAGACTT 60.004 57.895 0.00 0.00 38.60 3.01
117 118 2.659610 GGCACTCGCTGGAAGACT 59.340 61.111 0.00 0.00 38.60 3.24
118 119 2.811317 CGGCACTCGCTGGAAGAC 60.811 66.667 0.00 0.00 41.16 3.01
125 126 3.036084 CACGAAACGGCACTCGCT 61.036 61.111 0.00 0.00 43.89 4.93
126 127 4.719616 GCACGAAACGGCACTCGC 62.720 66.667 0.00 0.00 43.89 5.03
127 128 3.334751 TGCACGAAACGGCACTCG 61.335 61.111 0.00 0.00 45.88 4.18
131 132 2.818487 CTGTGTGCACGAAACGGCA 61.818 57.895 13.13 0.00 37.77 5.69
132 133 2.052237 CTGTGTGCACGAAACGGC 60.052 61.111 13.13 0.00 0.00 5.68
133 134 0.931702 TAACTGTGTGCACGAAACGG 59.068 50.000 13.13 12.42 0.00 4.44
134 135 1.325037 TGTAACTGTGTGCACGAAACG 59.675 47.619 13.13 4.52 0.00 3.60
135 136 2.700694 GTGTAACTGTGTGCACGAAAC 58.299 47.619 13.13 5.55 0.00 2.78
140 141 2.286184 CCTTTCGTGTAACTGTGTGCAC 60.286 50.000 10.75 10.75 31.75 4.57
141 142 1.937223 CCTTTCGTGTAACTGTGTGCA 59.063 47.619 0.00 0.00 31.75 4.57
142 143 1.333791 GCCTTTCGTGTAACTGTGTGC 60.334 52.381 0.00 0.00 31.75 4.57
143 144 1.937223 TGCCTTTCGTGTAACTGTGTG 59.063 47.619 0.00 0.00 31.75 3.82
144 145 1.937899 GTGCCTTTCGTGTAACTGTGT 59.062 47.619 0.00 0.00 31.75 3.72
145 146 2.210116 AGTGCCTTTCGTGTAACTGTG 58.790 47.619 0.00 0.00 31.75 3.66
146 147 2.480845 GAGTGCCTTTCGTGTAACTGT 58.519 47.619 0.00 0.00 31.75 3.55
147 148 1.455786 CGAGTGCCTTTCGTGTAACTG 59.544 52.381 0.00 0.00 33.57 3.16
148 149 1.338973 TCGAGTGCCTTTCGTGTAACT 59.661 47.619 2.28 0.00 39.05 2.24
149 150 1.719780 CTCGAGTGCCTTTCGTGTAAC 59.280 52.381 3.62 0.00 39.05 2.50
150 151 1.610038 TCTCGAGTGCCTTTCGTGTAA 59.390 47.619 13.13 0.00 39.05 2.41
151 152 1.241165 TCTCGAGTGCCTTTCGTGTA 58.759 50.000 13.13 0.00 39.05 2.90
152 153 0.603569 ATCTCGAGTGCCTTTCGTGT 59.396 50.000 13.13 0.00 39.05 4.49
153 154 2.561733 TATCTCGAGTGCCTTTCGTG 57.438 50.000 13.13 0.76 39.05 4.35
154 155 2.230508 TGTTATCTCGAGTGCCTTTCGT 59.769 45.455 13.13 0.00 39.05 3.85
155 156 2.876091 TGTTATCTCGAGTGCCTTTCG 58.124 47.619 13.13 0.00 39.33 3.46
156 157 3.371285 GGTTGTTATCTCGAGTGCCTTTC 59.629 47.826 13.13 0.29 0.00 2.62
157 158 3.335579 GGTTGTTATCTCGAGTGCCTTT 58.664 45.455 13.13 0.00 0.00 3.11
158 159 2.674177 CGGTTGTTATCTCGAGTGCCTT 60.674 50.000 13.13 0.00 0.00 4.35
159 160 1.135083 CGGTTGTTATCTCGAGTGCCT 60.135 52.381 13.13 0.00 0.00 4.75
160 161 1.135199 TCGGTTGTTATCTCGAGTGCC 60.135 52.381 13.13 4.74 0.00 5.01
161 162 2.273370 TCGGTTGTTATCTCGAGTGC 57.727 50.000 13.13 2.11 0.00 4.40
162 163 4.482386 TCTTTCGGTTGTTATCTCGAGTG 58.518 43.478 13.13 0.00 33.11 3.51
163 164 4.778534 TCTTTCGGTTGTTATCTCGAGT 57.221 40.909 13.13 2.46 33.11 4.18
164 165 6.263344 TGTATCTTTCGGTTGTTATCTCGAG 58.737 40.000 5.93 5.93 33.11 4.04
165 166 6.198650 TGTATCTTTCGGTTGTTATCTCGA 57.801 37.500 0.00 0.00 0.00 4.04
166 167 6.530534 ACTTGTATCTTTCGGTTGTTATCTCG 59.469 38.462 0.00 0.00 0.00 4.04
197 198 3.605634 TGTGGGCATATGATATTACGGC 58.394 45.455 6.97 0.00 0.00 5.68
215 220 4.992319 TGTGTCTAAAACCGTATCCTTGTG 59.008 41.667 0.00 0.00 0.00 3.33
384 396 1.945394 AGACCAGGTATACGTACGCAG 59.055 52.381 16.72 0.00 0.00 5.18
385 397 1.672363 CAGACCAGGTATACGTACGCA 59.328 52.381 16.72 1.76 0.00 5.24
386 398 1.002033 CCAGACCAGGTATACGTACGC 60.002 57.143 16.72 0.00 0.00 4.42
387 399 2.289002 GACCAGACCAGGTATACGTACG 59.711 54.545 15.01 15.01 43.38 3.67
417 434 2.237143 AGGATGTGTGATCGTTGATGGT 59.763 45.455 0.00 0.00 0.00 3.55
453 470 1.884926 GCTGCGGCAGAGATGGTAC 60.885 63.158 32.72 9.11 38.54 3.34
454 471 2.358372 TGCTGCGGCAGAGATGGTA 61.358 57.895 32.72 2.52 44.28 3.25
455 472 3.709633 TGCTGCGGCAGAGATGGT 61.710 61.111 32.72 0.00 44.28 3.55
524 541 2.455674 TGACTTGGAGTGATGAACGG 57.544 50.000 0.00 0.00 0.00 4.44
526 543 5.278022 GGTTTCTTGACTTGGAGTGATGAAC 60.278 44.000 0.00 0.00 28.55 3.18
588 615 3.114616 CTGGCTCGTTGCGGTGAG 61.115 66.667 0.00 0.00 44.05 3.51
801 884 0.451783 GACGGCTGGTTTATGGCAAG 59.548 55.000 0.00 0.00 0.00 4.01
947 1030 4.731853 TGGATGGTCAGGCGGGGA 62.732 66.667 0.00 0.00 0.00 4.81
1110 1202 4.394078 TCGTCGTCGAGGTTGGCG 62.394 66.667 14.08 4.73 41.35 5.69
1186 1294 2.170260 GAGCGAGAGAGCGATCGGAG 62.170 65.000 18.30 0.00 43.00 4.63
1378 1486 5.182570 TGGAGACAATTCAGCAGAATCAAAG 59.817 40.000 4.66 0.00 43.52 2.77
1479 1602 8.041143 ACCTATTAGTGGCATATAAGACCAAA 57.959 34.615 0.00 0.00 34.63 3.28
1642 1766 5.406477 GTCCAAATGACTTTTCTGAAATGGC 59.594 40.000 17.12 15.34 41.03 4.40
1712 1837 3.386726 CGGGAAGGACATACATAAGGACA 59.613 47.826 0.00 0.00 0.00 4.02
1713 1838 3.802675 GCGGGAAGGACATACATAAGGAC 60.803 52.174 0.00 0.00 0.00 3.85
1714 1839 2.367567 GCGGGAAGGACATACATAAGGA 59.632 50.000 0.00 0.00 0.00 3.36
1827 1953 2.342910 TTCCTTCGAACTGTACGAGC 57.657 50.000 0.00 0.00 40.72 5.03
1836 1978 9.447040 GTTGGCTATAATTATTTTCCTTCGAAC 57.553 33.333 2.68 1.02 0.00 3.95
1844 1986 9.343539 AGACTGGAGTTGGCTATAATTATTTTC 57.656 33.333 2.68 0.00 0.00 2.29
1880 2022 1.990060 CCACTGTGATCTCCCGGGT 60.990 63.158 22.86 0.00 0.00 5.28
1885 2027 2.939103 GCATAACACCACTGTGATCTCC 59.061 50.000 9.86 0.00 45.76 3.71
1888 2030 3.753272 ACAAGCATAACACCACTGTGATC 59.247 43.478 9.86 0.00 45.76 2.92
1911 2053 5.009510 CAGAGTAGTATACAGAGCTGCATGT 59.990 44.000 13.79 13.79 46.26 3.21
2152 2384 3.319137 TTGTGCTAGTTCCTACTGCAG 57.681 47.619 13.48 13.48 38.32 4.41
2153 2385 3.762407 TTTGTGCTAGTTCCTACTGCA 57.238 42.857 0.00 0.00 36.64 4.41
2195 2427 2.831685 AAGTCTTGCATACACGACCA 57.168 45.000 0.00 0.00 44.08 4.02
2260 2492 6.493978 AGTTTTTGGCACATTAAAACATTGC 58.506 32.000 20.99 1.52 45.86 3.56
2433 2665 6.607004 ACGGAGGGAGTATCTTATAAATGG 57.393 41.667 0.00 0.00 33.73 3.16
2449 2681 4.995487 GCTCCTATATTTGTTTACGGAGGG 59.005 45.833 0.00 0.00 37.59 4.30
2450 2682 4.684703 CGCTCCTATATTTGTTTACGGAGG 59.315 45.833 0.00 0.00 37.59 4.30
2451 2683 5.287226 ACGCTCCTATATTTGTTTACGGAG 58.713 41.667 0.00 0.00 39.55 4.63
2453 2685 5.978934 AACGCTCCTATATTTGTTTACGG 57.021 39.130 0.00 0.00 0.00 4.02
2454 2686 8.343974 TCTAAACGCTCCTATATTTGTTTACG 57.656 34.615 0.00 0.00 32.41 3.18
2457 2689 8.827677 GTGATCTAAACGCTCCTATATTTGTTT 58.172 33.333 0.00 0.00 34.32 2.83
2458 2690 8.204836 AGTGATCTAAACGCTCCTATATTTGTT 58.795 33.333 0.00 0.00 0.00 2.83
2459 2691 7.727181 AGTGATCTAAACGCTCCTATATTTGT 58.273 34.615 0.00 0.00 0.00 2.83
2460 2692 9.692749 TTAGTGATCTAAACGCTCCTATATTTG 57.307 33.333 0.00 0.00 33.79 2.32
2465 2697 9.614792 AAATTTTAGTGATCTAAACGCTCCTAT 57.385 29.630 0.00 0.00 43.20 2.57
2466 2698 8.879759 CAAATTTTAGTGATCTAAACGCTCCTA 58.120 33.333 0.00 0.00 43.20 2.94
2467 2699 7.148239 CCAAATTTTAGTGATCTAAACGCTCCT 60.148 37.037 0.00 0.00 43.20 3.69
2468 2700 6.967199 CCAAATTTTAGTGATCTAAACGCTCC 59.033 38.462 0.00 0.00 43.20 4.70
2469 2701 6.967199 CCCAAATTTTAGTGATCTAAACGCTC 59.033 38.462 0.00 0.00 43.20 5.03
2470 2702 6.433093 ACCCAAATTTTAGTGATCTAAACGCT 59.567 34.615 0.00 0.00 43.20 5.07
2471 2703 6.526674 CACCCAAATTTTAGTGATCTAAACGC 59.473 38.462 10.54 0.00 43.20 4.84
2472 2704 6.526674 GCACCCAAATTTTAGTGATCTAAACG 59.473 38.462 17.55 0.00 43.20 3.60
2473 2705 7.328493 GTGCACCCAAATTTTAGTGATCTAAAC 59.672 37.037 17.55 3.12 43.20 2.01
2474 2706 7.375053 GTGCACCCAAATTTTAGTGATCTAAA 58.625 34.615 17.55 0.00 42.24 1.85
2475 2707 6.071616 GGTGCACCCAAATTTTAGTGATCTAA 60.072 38.462 26.31 0.00 34.76 2.10
2476 2708 5.417580 GGTGCACCCAAATTTTAGTGATCTA 59.582 40.000 26.31 2.47 31.79 1.98
2477 2709 4.220602 GGTGCACCCAAATTTTAGTGATCT 59.779 41.667 26.31 0.00 31.79 2.75
2478 2710 4.494484 GGTGCACCCAAATTTTAGTGATC 58.506 43.478 26.31 10.54 31.79 2.92
2479 2711 4.535526 GGTGCACCCAAATTTTAGTGAT 57.464 40.909 26.31 0.00 31.79 3.06
2549 2781 7.349859 TGGAGTGGGGTTATAAACTCATAAGAT 59.650 37.037 6.31 0.00 40.67 2.40
2748 2984 5.721232 AGAACTAGTGATTGTCCTAAACCG 58.279 41.667 0.00 0.00 0.00 4.44
2886 3122 6.990908 TCTATGGCATATCCTGGATATCTG 57.009 41.667 23.27 16.95 33.52 2.90
2893 3129 6.966534 AAAAAGTTCTATGGCATATCCTGG 57.033 37.500 7.81 0.00 35.26 4.45
2895 3131 7.816411 ACCTAAAAAGTTCTATGGCATATCCT 58.184 34.615 7.81 1.57 35.26 3.24
3325 3683 3.181506 GCACTAGCACCTGTAGCATTTTC 60.182 47.826 0.00 0.00 41.58 2.29
3456 3814 2.618241 TCGCCATGACCAAATGATTAGC 59.382 45.455 0.00 0.00 0.00 3.09
3622 3981 6.371825 TCTCTTCGCGACATCATATACTATGT 59.628 38.462 9.15 2.23 39.00 2.29
3635 3994 0.675208 AGCTCTCTCTCTTCGCGACA 60.675 55.000 9.15 0.00 0.00 4.35
3763 4122 9.243637 TCAGGAAAAATAACAATTTCTGTTTCG 57.756 29.630 0.00 0.00 46.49 3.46
3821 4184 9.869757 AAAGTTGTGTAGAAAAAGCAATTTAGT 57.130 25.926 0.00 0.00 0.00 2.24
3928 4292 4.081752 GTGACTGTTCTCTCATCATCCTGT 60.082 45.833 0.00 0.00 0.00 4.00
3973 4337 3.244665 ACAGACATCCAGATTCTTGTGCA 60.245 43.478 0.00 0.00 0.00 4.57
4117 4482 6.686126 GCCCCATGTGTTTGCATCTTAATAAT 60.686 38.462 0.00 0.00 0.00 1.28
4118 4483 5.395103 GCCCCATGTGTTTGCATCTTAATAA 60.395 40.000 0.00 0.00 0.00 1.40
4119 4484 4.099266 GCCCCATGTGTTTGCATCTTAATA 59.901 41.667 0.00 0.00 0.00 0.98
4175 4541 5.763204 CCTACTAGAAGAAAAAGCAACCACA 59.237 40.000 0.00 0.00 0.00 4.17
4193 4559 4.811498 TGTATCTAAGGGCTTGCCTACTA 58.189 43.478 11.71 0.54 0.00 1.82
4207 4573 9.371136 GAGTCTGTTTGTGATTCATGTATCTAA 57.629 33.333 12.82 6.28 0.00 2.10
4211 4577 7.164122 ACTGAGTCTGTTTGTGATTCATGTAT 58.836 34.615 0.00 0.00 31.52 2.29
4241 4781 1.215382 CAAGGATCTGCACGACGGA 59.785 57.895 0.00 0.00 38.30 4.69
4369 4909 2.541794 GCGAGCTCAATCATACTCACGA 60.542 50.000 15.40 0.00 0.00 4.35
4370 4910 1.783711 GCGAGCTCAATCATACTCACG 59.216 52.381 15.40 0.00 0.00 4.35
4489 5030 4.164204 CCCAATTTCCCCACCTTTTCTAA 58.836 43.478 0.00 0.00 0.00 2.10
4632 5288 1.902508 GGAAGGTCTGTCTCATCACCA 59.097 52.381 0.00 0.00 0.00 4.17
4635 5291 2.630889 AGGGAAGGTCTGTCTCATCA 57.369 50.000 0.00 0.00 0.00 3.07
4685 5341 2.741985 TTCAGTGCCGTCCATGCG 60.742 61.111 0.00 0.00 0.00 4.73
4814 5470 2.036256 CACTTCCCCTGGCCCTTG 59.964 66.667 0.00 0.00 0.00 3.61
4831 5487 0.922626 AAGGGAAGGATGGCCTCTTC 59.077 55.000 19.05 19.05 46.28 2.87
4843 5499 1.885887 TGGAAAATGTGCGAAGGGAAG 59.114 47.619 0.00 0.00 0.00 3.46
4846 5502 1.533625 TCTGGAAAATGTGCGAAGGG 58.466 50.000 0.00 0.00 0.00 3.95
4854 5510 3.509442 TGCTGGGAAATCTGGAAAATGT 58.491 40.909 0.00 0.00 0.00 2.71
4921 5596 3.249189 TGGGCTCTTCGGCACCTT 61.249 61.111 0.00 0.00 40.61 3.50
4943 5618 6.293626 CCGGGCTTGAAAACATTGATCTATAG 60.294 42.308 0.00 0.00 0.00 1.31
4961 5636 0.250338 GTCAAGTGAACTCCGGGCTT 60.250 55.000 0.00 0.00 0.00 4.35
5011 5686 1.886886 TTGCGGTTAGGGTTCAGTTC 58.113 50.000 0.00 0.00 0.00 3.01
5051 5726 2.922740 TAAGTGGAACAAAGACGCCT 57.077 45.000 0.00 0.00 44.16 5.52
5055 5730 5.182001 ACATCAGCATAAGTGGAACAAAGAC 59.818 40.000 0.00 0.00 44.16 3.01
5146 5821 4.040755 AGTACCTGATACTTTCCCATGCT 58.959 43.478 0.00 0.00 41.71 3.79
5268 5944 9.191479 TGGACCTGAAATTTTTAGAAGTTGTAA 57.809 29.630 2.68 0.00 0.00 2.41
5275 5951 8.754080 TCAAGTTTGGACCTGAAATTTTTAGAA 58.246 29.630 2.68 0.00 0.00 2.10
5276 5952 8.299990 TCAAGTTTGGACCTGAAATTTTTAGA 57.700 30.769 2.68 0.00 0.00 2.10
5321 8303 6.183360 ACACTATTCATGCCAGATTTCACATG 60.183 38.462 0.00 0.00 40.97 3.21



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

AutoCloner maintained by Alex Coulton.