Multiple sequence alignment - TraesCS6D01G404500

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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 TraesCS6D01G404500 chr6D 100.000 3149 0 0 1 3149 472307438 472304290 0.000000e+00 5816.0
1 TraesCS6D01G404500 chr6A 91.015 1625 92 37 586 2199 617685854 617687435 0.000000e+00 2143.0
2 TraesCS6D01G404500 chr6A 93.023 258 17 1 2893 3149 617688604 617688861 2.970000e-100 375.0
3 TraesCS6D01G404500 chr6A 89.370 254 25 2 2264 2515 617687723 617687976 5.070000e-83 318.0
4 TraesCS6D01G404500 chr6A 92.969 128 9 0 2512 2639 617688097 617688224 1.490000e-43 187.0
5 TraesCS6D01G404500 chr6A 92.157 51 4 0 187 237 617685628 617685678 4.360000e-09 73.1
6 TraesCS6D01G404500 chr6B 91.933 1376 64 14 820 2192 716976900 716975569 0.000000e+00 1882.0
7 TraesCS6D01G404500 chr6B 87.485 831 79 19 2340 3149 716975352 716974526 0.000000e+00 935.0
8 TraesCS6D01G404500 chr6B 84.245 457 37 8 2414 2851 699123836 699123396 2.260000e-111 412.0
9 TraesCS6D01G404500 chr6B 85.235 149 9 7 1 148 129520999 129521135 1.180000e-29 141.0
10 TraesCS6D01G404500 chr6B 96.429 56 2 0 2262 2317 716975406 716975351 3.340000e-15 93.5
11 TraesCS6D01G404500 chr2B 87.459 1212 131 11 945 2155 691452942 691451751 0.000000e+00 1376.0
12 TraesCS6D01G404500 chr2B 79.417 515 56 24 371 841 691453533 691453025 5.070000e-83 318.0
13 TraesCS6D01G404500 chr2B 81.781 247 24 9 1 246 649865051 649865277 1.490000e-43 187.0
14 TraesCS6D01G404500 chr2B 92.000 100 8 0 1 100 64654689 64654788 1.180000e-29 141.0
15 TraesCS6D01G404500 chr2B 84.564 149 10 7 1 148 64726207 64726343 5.480000e-28 135.0
16 TraesCS6D01G404500 chr2D 87.376 1212 129 11 945 2155 575359357 575358169 0.000000e+00 1369.0
17 TraesCS6D01G404500 chr2D 83.649 581 47 21 240 798 140713690 140713136 1.300000e-138 503.0
18 TraesCS6D01G404500 chr2A 87.017 1217 131 15 945 2155 713543614 713542419 0.000000e+00 1347.0
19 TraesCS6D01G404500 chr2A 79.604 505 49 24 374 841 713544191 713543704 2.360000e-81 313.0
20 TraesCS6D01G404500 chr1D 84.075 584 43 22 240 798 432956220 432955662 4.660000e-143 518.0
21 TraesCS6D01G404500 chr7D 84.083 578 47 20 242 798 26614383 26614936 1.670000e-142 516.0
22 TraesCS6D01G404500 chr7D 82.933 375 40 15 440 798 73007844 73007478 1.820000e-82 316.0
23 TraesCS6D01G404500 chr7D 82.933 375 39 19 440 798 190196590 190196225 6.560000e-82 315.0
24 TraesCS6D01G404500 chr1B 83.040 454 42 8 2414 2848 665782040 665782477 2.290000e-101 379.0
25 TraesCS6D01G404500 chrUn 83.200 375 39 16 440 798 96713153 96713519 3.920000e-84 322.0
26 TraesCS6D01G404500 chr4D 82.667 375 41 15 440 798 21034715 21035081 8.480000e-81 311.0
27 TraesCS6D01G404500 chr3D 85.050 301 22 14 278 576 540179161 540178882 5.140000e-73 285.0
28 TraesCS6D01G404500 chr3D 90.196 51 3 1 153 201 540179216 540179166 7.290000e-07 65.8
29 TraesCS6D01G404500 chr7A 84.158 303 21 14 273 573 95652995 95652718 5.180000e-68 268.0
30 TraesCS6D01G404500 chr4A 82.591 247 22 11 1 246 691714590 691714816 6.890000e-47 198.0
31 TraesCS6D01G404500 chr4B 92.000 100 8 0 1 100 577380670 577380769 1.180000e-29 141.0
32 TraesCS6D01G404500 chr4B 93.407 91 6 0 10 100 162811069 162810979 5.480000e-28 135.0
33 TraesCS6D01G404500 chr4B 84.564 149 10 7 1 148 222501721 222501857 5.480000e-28 135.0
34 TraesCS6D01G404500 chr7B 84.564 149 10 7 1 148 129221296 129221432 5.480000e-28 135.0
35 TraesCS6D01G404500 chr7B 84.564 149 10 7 1 148 649188806 649188942 5.480000e-28 135.0
36 TraesCS6D01G404500 chr5B 89.109 101 9 2 382 481 674553440 674553341 1.190000e-24 124.0


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 TraesCS6D01G404500 chr6D 472304290 472307438 3148 True 5816.000000 5816 100.0000 1 3149 1 chr6D.!!$R1 3148
1 TraesCS6D01G404500 chr6A 617685628 617688861 3233 False 619.220000 2143 91.7068 187 3149 5 chr6A.!!$F1 2962
2 TraesCS6D01G404500 chr6B 716974526 716976900 2374 True 970.166667 1882 91.9490 820 3149 3 chr6B.!!$R2 2329
3 TraesCS6D01G404500 chr2B 691451751 691453533 1782 True 847.000000 1376 83.4380 371 2155 2 chr2B.!!$R1 1784
4 TraesCS6D01G404500 chr2D 575358169 575359357 1188 True 1369.000000 1369 87.3760 945 2155 1 chr2D.!!$R2 1210
5 TraesCS6D01G404500 chr2D 140713136 140713690 554 True 503.000000 503 83.6490 240 798 1 chr2D.!!$R1 558
6 TraesCS6D01G404500 chr2A 713542419 713544191 1772 True 830.000000 1347 83.3105 374 2155 2 chr2A.!!$R1 1781
7 TraesCS6D01G404500 chr1D 432955662 432956220 558 True 518.000000 518 84.0750 240 798 1 chr1D.!!$R1 558
8 TraesCS6D01G404500 chr7D 26614383 26614936 553 False 516.000000 516 84.0830 242 798 1 chr7D.!!$F1 556

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
39 40 0.037975 GTTCATGGCTGCCTGGTTTG 60.038 55.0 21.03 9.59 0.0 2.93 F
186 187 0.111061 AGTGAGCAACAGATGGGCAA 59.889 50.0 0.00 0.00 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 2120 1.202330 CCTCTCCCTCAATGACAGCT 58.798 55.000 0.00 0.00 0.0 4.24 R
2151 2273 4.707934 AGACAAGAAAGGTACCTCTCTAGC 59.292 45.833 18.28 10.35 0.0 3.42 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
19 20 2.869233 AAACTGAGCACACGCAAATT 57.131 40.000 0.00 0.00 42.27 1.82
20 21 2.124011 AACTGAGCACACGCAAATTG 57.876 45.000 0.00 0.00 42.27 2.32
21 22 1.024271 ACTGAGCACACGCAAATTGT 58.976 45.000 0.00 0.00 42.27 2.71
22 23 1.405105 ACTGAGCACACGCAAATTGTT 59.595 42.857 0.00 0.00 42.27 2.83
23 24 2.046313 CTGAGCACACGCAAATTGTTC 58.954 47.619 0.00 0.00 42.27 3.18
24 25 1.403323 TGAGCACACGCAAATTGTTCA 59.597 42.857 0.00 0.00 42.27 3.18
25 26 2.034432 TGAGCACACGCAAATTGTTCAT 59.966 40.909 0.00 0.00 42.27 2.57
26 27 2.396601 AGCACACGCAAATTGTTCATG 58.603 42.857 0.00 0.00 42.27 3.07
27 28 1.456544 GCACACGCAAATTGTTCATGG 59.543 47.619 0.00 0.00 38.36 3.66
28 29 1.456544 CACACGCAAATTGTTCATGGC 59.543 47.619 0.00 0.00 0.00 4.40
29 30 1.340889 ACACGCAAATTGTTCATGGCT 59.659 42.857 0.00 0.00 0.00 4.75
30 31 1.722464 CACGCAAATTGTTCATGGCTG 59.278 47.619 0.00 0.00 0.00 4.85
31 32 0.717224 CGCAAATTGTTCATGGCTGC 59.283 50.000 0.00 0.00 0.00 5.25
32 33 1.081094 GCAAATTGTTCATGGCTGCC 58.919 50.000 12.87 12.87 0.00 4.85
33 34 1.338389 GCAAATTGTTCATGGCTGCCT 60.338 47.619 21.03 2.27 0.00 4.75
34 35 2.343101 CAAATTGTTCATGGCTGCCTG 58.657 47.619 21.03 15.05 0.00 4.85
35 36 0.899720 AATTGTTCATGGCTGCCTGG 59.100 50.000 21.03 11.85 0.00 4.45
36 37 0.251922 ATTGTTCATGGCTGCCTGGT 60.252 50.000 21.03 2.98 0.00 4.00
37 38 0.469705 TTGTTCATGGCTGCCTGGTT 60.470 50.000 21.03 0.00 0.00 3.67
38 39 0.469705 TGTTCATGGCTGCCTGGTTT 60.470 50.000 21.03 0.00 0.00 3.27
39 40 0.037975 GTTCATGGCTGCCTGGTTTG 60.038 55.000 21.03 9.59 0.00 2.93
40 41 0.178967 TTCATGGCTGCCTGGTTTGA 60.179 50.000 21.03 11.65 0.00 2.69
41 42 0.895100 TCATGGCTGCCTGGTTTGAC 60.895 55.000 21.03 0.00 0.00 3.18
42 43 1.607467 ATGGCTGCCTGGTTTGACC 60.607 57.895 21.03 0.00 39.22 4.02
43 44 3.365265 GGCTGCCTGGTTTGACCG 61.365 66.667 12.43 0.00 42.58 4.79
44 45 2.281484 GCTGCCTGGTTTGACCGA 60.281 61.111 0.00 0.00 42.58 4.69
45 46 1.675641 GCTGCCTGGTTTGACCGAT 60.676 57.895 0.00 0.00 42.58 4.18
46 47 1.648467 GCTGCCTGGTTTGACCGATC 61.648 60.000 0.00 0.00 42.58 3.69
47 48 1.002624 TGCCTGGTTTGACCGATCC 60.003 57.895 0.00 0.00 42.58 3.36
48 49 1.002624 GCCTGGTTTGACCGATCCA 60.003 57.895 0.00 0.00 42.58 3.41
49 50 1.026718 GCCTGGTTTGACCGATCCAG 61.027 60.000 7.20 7.20 42.58 3.86
53 54 3.433306 TGGTTTGACCGATCCAGAATT 57.567 42.857 0.00 0.00 42.58 2.17
54 55 4.561500 TGGTTTGACCGATCCAGAATTA 57.438 40.909 0.00 0.00 42.58 1.40
55 56 5.110814 TGGTTTGACCGATCCAGAATTAT 57.889 39.130 0.00 0.00 42.58 1.28
56 57 4.881273 TGGTTTGACCGATCCAGAATTATG 59.119 41.667 0.00 0.00 42.58 1.90
57 58 4.275936 GGTTTGACCGATCCAGAATTATGG 59.724 45.833 13.14 13.14 42.11 2.74
65 66 3.627395 TCCAGAATTATGGACGCTGTT 57.373 42.857 17.86 0.00 44.56 3.16
66 67 3.270027 TCCAGAATTATGGACGCTGTTG 58.730 45.455 17.86 0.00 44.56 3.33
67 68 2.355756 CCAGAATTATGGACGCTGTTGG 59.644 50.000 14.13 0.00 43.57 3.77
68 69 3.009723 CAGAATTATGGACGCTGTTGGT 58.990 45.455 0.00 0.00 0.00 3.67
69 70 3.440173 CAGAATTATGGACGCTGTTGGTT 59.560 43.478 0.00 0.00 0.00 3.67
70 71 3.689649 AGAATTATGGACGCTGTTGGTTC 59.310 43.478 0.00 0.00 0.00 3.62
71 72 2.851263 TTATGGACGCTGTTGGTTCT 57.149 45.000 0.00 0.00 0.00 3.01
72 73 2.093306 TATGGACGCTGTTGGTTCTG 57.907 50.000 0.00 0.00 0.00 3.02
73 74 0.396435 ATGGACGCTGTTGGTTCTGA 59.604 50.000 0.00 0.00 0.00 3.27
74 75 0.179234 TGGACGCTGTTGGTTCTGAA 59.821 50.000 0.00 0.00 0.00 3.02
75 76 0.586802 GGACGCTGTTGGTTCTGAAC 59.413 55.000 12.05 12.05 0.00 3.18
96 97 3.924922 CCTAGGTAGGGGACATGTAAGT 58.075 50.000 0.00 0.00 39.86 2.24
97 98 5.070823 CCTAGGTAGGGGACATGTAAGTA 57.929 47.826 0.00 0.00 39.86 2.24
98 99 5.078256 CCTAGGTAGGGGACATGTAAGTAG 58.922 50.000 0.00 0.00 39.86 2.57
99 100 3.306613 AGGTAGGGGACATGTAAGTAGC 58.693 50.000 0.00 0.00 0.00 3.58
100 101 3.052033 AGGTAGGGGACATGTAAGTAGCT 60.052 47.826 0.00 0.70 0.00 3.32
101 102 4.169461 AGGTAGGGGACATGTAAGTAGCTA 59.831 45.833 0.00 0.00 0.00 3.32
102 103 4.523558 GGTAGGGGACATGTAAGTAGCTAG 59.476 50.000 0.00 0.00 0.00 3.42
103 104 4.267341 AGGGGACATGTAAGTAGCTAGT 57.733 45.455 0.00 0.00 0.00 2.57
104 105 4.216708 AGGGGACATGTAAGTAGCTAGTC 58.783 47.826 0.00 0.03 0.00 2.59
105 106 3.958798 GGGGACATGTAAGTAGCTAGTCA 59.041 47.826 0.00 0.00 0.00 3.41
106 107 4.404715 GGGGACATGTAAGTAGCTAGTCAA 59.595 45.833 0.00 0.00 0.00 3.18
107 108 5.070580 GGGGACATGTAAGTAGCTAGTCAAT 59.929 44.000 0.00 0.00 0.00 2.57
108 109 6.408206 GGGGACATGTAAGTAGCTAGTCAATT 60.408 42.308 0.00 0.00 0.00 2.32
109 110 7.201974 GGGGACATGTAAGTAGCTAGTCAATTA 60.202 40.741 0.00 0.00 0.00 1.40
110 111 7.868415 GGGACATGTAAGTAGCTAGTCAATTAG 59.132 40.741 0.00 0.00 0.00 1.73
111 112 7.382759 GGACATGTAAGTAGCTAGTCAATTAGC 59.617 40.741 0.00 0.00 45.05 3.09
112 113 7.210873 ACATGTAAGTAGCTAGTCAATTAGCC 58.789 38.462 0.44 0.00 45.69 3.93
113 114 6.158023 TGTAAGTAGCTAGTCAATTAGCCC 57.842 41.667 0.44 0.00 45.69 5.19
114 115 4.691326 AAGTAGCTAGTCAATTAGCCCC 57.309 45.455 0.44 0.00 45.69 5.80
115 116 3.930035 AGTAGCTAGTCAATTAGCCCCT 58.070 45.455 0.00 0.00 45.69 4.79
116 117 4.299485 AGTAGCTAGTCAATTAGCCCCTT 58.701 43.478 0.00 0.00 45.69 3.95
117 118 4.722279 AGTAGCTAGTCAATTAGCCCCTTT 59.278 41.667 0.00 0.00 45.69 3.11
118 119 3.891049 AGCTAGTCAATTAGCCCCTTTG 58.109 45.455 1.36 0.00 45.69 2.77
119 120 2.359214 GCTAGTCAATTAGCCCCTTTGC 59.641 50.000 0.00 0.00 40.10 3.68
120 121 2.907458 AGTCAATTAGCCCCTTTGCT 57.093 45.000 0.00 0.00 45.38 3.91
121 122 2.450476 AGTCAATTAGCCCCTTTGCTG 58.550 47.619 0.00 0.00 42.77 4.41
122 123 1.134995 GTCAATTAGCCCCTTTGCTGC 60.135 52.381 0.00 0.00 42.77 5.25
123 124 0.176449 CAATTAGCCCCTTTGCTGCC 59.824 55.000 0.00 0.00 42.77 4.85
124 125 1.322538 AATTAGCCCCTTTGCTGCCG 61.323 55.000 0.00 0.00 42.77 5.69
125 126 3.936772 TTAGCCCCTTTGCTGCCGG 62.937 63.158 0.00 0.00 42.77 6.13
135 136 3.590824 GCTGCCGGCACAGTTTAT 58.409 55.556 29.03 0.00 39.96 1.40
136 137 1.429423 GCTGCCGGCACAGTTTATC 59.571 57.895 29.03 0.00 39.96 1.75
137 138 1.026718 GCTGCCGGCACAGTTTATCT 61.027 55.000 29.03 0.00 39.96 1.98
138 139 1.742411 GCTGCCGGCACAGTTTATCTA 60.742 52.381 29.03 0.00 39.96 1.98
139 140 2.205074 CTGCCGGCACAGTTTATCTAG 58.795 52.381 29.03 7.36 32.78 2.43
140 141 0.938008 GCCGGCACAGTTTATCTAGC 59.062 55.000 24.80 0.00 0.00 3.42
141 142 1.742411 GCCGGCACAGTTTATCTAGCA 60.742 52.381 24.80 0.00 0.00 3.49
142 143 2.627945 CCGGCACAGTTTATCTAGCAA 58.372 47.619 0.00 0.00 0.00 3.91
143 144 3.006940 CCGGCACAGTTTATCTAGCAAA 58.993 45.455 0.00 0.00 0.00 3.68
144 145 3.627577 CCGGCACAGTTTATCTAGCAAAT 59.372 43.478 0.00 0.00 0.00 2.32
145 146 4.096382 CCGGCACAGTTTATCTAGCAAATT 59.904 41.667 0.00 0.00 0.00 1.82
146 147 5.295787 CCGGCACAGTTTATCTAGCAAATTA 59.704 40.000 0.00 0.00 0.00 1.40
147 148 6.183360 CCGGCACAGTTTATCTAGCAAATTAA 60.183 38.462 0.00 0.00 0.00 1.40
148 149 7.247728 CGGCACAGTTTATCTAGCAAATTAAA 58.752 34.615 0.00 0.00 0.00 1.52
149 150 7.218204 CGGCACAGTTTATCTAGCAAATTAAAC 59.782 37.037 0.00 0.00 0.00 2.01
150 151 8.026607 GGCACAGTTTATCTAGCAAATTAAACA 58.973 33.333 12.08 0.00 31.90 2.83
151 152 8.850452 GCACAGTTTATCTAGCAAATTAAACAC 58.150 33.333 12.08 0.00 31.90 3.32
152 153 9.891828 CACAGTTTATCTAGCAAATTAAACACA 57.108 29.630 12.08 0.00 31.90 3.72
173 174 8.879342 ACACATACTAGAATTTATGAGTGAGC 57.121 34.615 0.00 0.00 31.00 4.26
174 175 8.478066 ACACATACTAGAATTTATGAGTGAGCA 58.522 33.333 0.00 0.00 31.00 4.26
175 176 9.317936 CACATACTAGAATTTATGAGTGAGCAA 57.682 33.333 0.00 0.00 31.28 3.91
176 177 9.319143 ACATACTAGAATTTATGAGTGAGCAAC 57.681 33.333 0.00 0.00 31.28 4.17
177 178 9.317936 CATACTAGAATTTATGAGTGAGCAACA 57.682 33.333 0.00 0.00 0.00 3.33
178 179 7.840342 ACTAGAATTTATGAGTGAGCAACAG 57.160 36.000 0.00 0.00 0.00 3.16
179 180 7.615403 ACTAGAATTTATGAGTGAGCAACAGA 58.385 34.615 0.00 0.00 0.00 3.41
180 181 8.263640 ACTAGAATTTATGAGTGAGCAACAGAT 58.736 33.333 0.00 0.00 0.00 2.90
181 182 7.317842 AGAATTTATGAGTGAGCAACAGATG 57.682 36.000 0.00 0.00 0.00 2.90
182 183 6.318144 AGAATTTATGAGTGAGCAACAGATGG 59.682 38.462 0.00 0.00 0.00 3.51
183 184 2.414994 ATGAGTGAGCAACAGATGGG 57.585 50.000 0.00 0.00 0.00 4.00
184 185 0.321919 TGAGTGAGCAACAGATGGGC 60.322 55.000 0.00 0.00 0.00 5.36
185 186 0.321919 GAGTGAGCAACAGATGGGCA 60.322 55.000 0.00 0.00 0.00 5.36
186 187 0.111061 AGTGAGCAACAGATGGGCAA 59.889 50.000 0.00 0.00 0.00 4.52
187 188 0.961019 GTGAGCAACAGATGGGCAAA 59.039 50.000 0.00 0.00 0.00 3.68
188 189 1.340889 GTGAGCAACAGATGGGCAAAA 59.659 47.619 0.00 0.00 0.00 2.44
189 190 1.614903 TGAGCAACAGATGGGCAAAAG 59.385 47.619 0.00 0.00 0.00 2.27
190 191 1.888512 GAGCAACAGATGGGCAAAAGA 59.111 47.619 0.00 0.00 0.00 2.52
191 192 2.297033 GAGCAACAGATGGGCAAAAGAA 59.703 45.455 0.00 0.00 0.00 2.52
192 193 2.036346 AGCAACAGATGGGCAAAAGAAC 59.964 45.455 0.00 0.00 0.00 3.01
193 194 2.224018 GCAACAGATGGGCAAAAGAACA 60.224 45.455 0.00 0.00 0.00 3.18
194 195 3.555586 GCAACAGATGGGCAAAAGAACAT 60.556 43.478 0.00 0.00 0.00 2.71
195 196 4.240096 CAACAGATGGGCAAAAGAACATC 58.760 43.478 0.00 0.00 39.89 3.06
196 197 3.499338 ACAGATGGGCAAAAGAACATCA 58.501 40.909 0.00 0.00 41.55 3.07
197 198 3.508793 ACAGATGGGCAAAAGAACATCAG 59.491 43.478 0.00 0.00 41.55 2.90
198 199 2.494870 AGATGGGCAAAAGAACATCAGC 59.505 45.455 0.00 0.00 41.55 4.26
237 238 1.354040 GTGGAGATTCTGTGTCGCAG 58.646 55.000 7.09 7.09 46.34 5.18
238 239 0.390340 TGGAGATTCTGTGTCGCAGC 60.390 55.000 8.61 0.00 44.66 5.25
253 254 1.008538 CAGCCGTGAACCAAACTGC 60.009 57.895 0.00 0.00 0.00 4.40
303 309 1.731160 CAGAGTAGAGCTTGCAGCAAC 59.269 52.381 2.83 1.60 45.56 4.17
338 344 8.204160 TCTGAATTCTGAAACTCTCTAACAACA 58.796 33.333 12.17 0.00 0.00 3.33
339 345 8.370493 TGAATTCTGAAACTCTCTAACAACAG 57.630 34.615 7.05 0.00 0.00 3.16
340 346 8.204160 TGAATTCTGAAACTCTCTAACAACAGA 58.796 33.333 7.05 0.00 0.00 3.41
341 347 8.600449 AATTCTGAAACTCTCTAACAACAGAG 57.400 34.615 0.00 0.00 42.96 3.35
342 348 5.533482 TCTGAAACTCTCTAACAACAGAGC 58.467 41.667 0.00 0.00 41.61 4.09
343 349 5.069119 TCTGAAACTCTCTAACAACAGAGCA 59.931 40.000 0.00 0.00 41.61 4.26
344 350 5.292765 TGAAACTCTCTAACAACAGAGCAG 58.707 41.667 0.00 0.00 41.61 4.24
345 351 5.069119 TGAAACTCTCTAACAACAGAGCAGA 59.931 40.000 0.00 0.00 41.61 4.26
346 352 4.782019 ACTCTCTAACAACAGAGCAGAG 57.218 45.455 0.00 0.00 41.61 3.35
347 353 3.056891 ACTCTCTAACAACAGAGCAGAGC 60.057 47.826 0.00 0.00 41.61 4.09
348 354 2.893489 TCTCTAACAACAGAGCAGAGCA 59.107 45.455 0.00 0.00 41.61 4.26
349 355 3.056962 TCTCTAACAACAGAGCAGAGCAG 60.057 47.826 0.00 0.00 41.61 4.24
350 356 2.893489 TCTAACAACAGAGCAGAGCAGA 59.107 45.455 0.00 0.00 0.00 4.26
351 357 2.166821 AACAACAGAGCAGAGCAGAG 57.833 50.000 0.00 0.00 0.00 3.35
352 358 1.047002 ACAACAGAGCAGAGCAGAGT 58.953 50.000 0.00 0.00 0.00 3.24
411 418 2.899303 ACCATTCGAATTCCCAGGTT 57.101 45.000 8.21 0.00 0.00 3.50
415 422 3.129287 CCATTCGAATTCCCAGGTTCAAG 59.871 47.826 8.21 0.00 0.00 3.02
470 484 0.468585 GCCATGGATCCAGATGCCAA 60.469 55.000 21.33 0.00 34.95 4.52
472 486 2.168496 CCATGGATCCAGATGCCAATC 58.832 52.381 21.33 0.00 34.95 2.67
474 488 2.945080 TGGATCCAGATGCCAATCTC 57.055 50.000 11.44 0.00 41.43 2.75
476 491 2.781757 TGGATCCAGATGCCAATCTCTT 59.218 45.455 11.44 0.00 41.43 2.85
504 523 3.209410 GAAGCTACAAGGGGATGATGTG 58.791 50.000 0.00 0.00 0.00 3.21
509 528 3.634397 ACAAGGGGATGATGTGTGTAG 57.366 47.619 0.00 0.00 0.00 2.74
510 529 2.912956 ACAAGGGGATGATGTGTGTAGT 59.087 45.455 0.00 0.00 0.00 2.73
511 530 3.330701 ACAAGGGGATGATGTGTGTAGTT 59.669 43.478 0.00 0.00 0.00 2.24
539 564 1.661509 CTTGTCGACGCAGCTGTCA 60.662 57.895 16.64 3.01 38.84 3.58
662 697 1.189752 TCTCTCCATGGTCAGAGCAC 58.810 55.000 20.77 0.00 36.79 4.40
668 714 2.306805 TCCATGGTCAGAGCACAAAGAT 59.693 45.455 12.58 0.00 0.00 2.40
672 718 5.366460 CATGGTCAGAGCACAAAGATATCT 58.634 41.667 3.92 0.00 0.00 1.98
720 784 1.287730 GCTCACAGTCGCAGTTGAGG 61.288 60.000 0.00 0.00 0.00 3.86
847 937 2.520741 GTTGGTGGTGGTGGTGGG 60.521 66.667 0.00 0.00 0.00 4.61
880 980 1.598962 CCACACCTGTCAGCCACTG 60.599 63.158 0.00 0.00 0.00 3.66
882 982 1.146930 ACACCTGTCAGCCACTGTG 59.853 57.895 0.00 0.00 35.65 3.66
1111 1233 2.125350 CGACCAAGCTCAGAGCCC 60.125 66.667 19.40 2.89 43.77 5.19
1263 1385 3.062466 CTCTCCCTCGGCGACACA 61.062 66.667 4.99 0.00 0.00 3.72
1887 2009 1.909376 CGATGTCGTCCGACTTCATT 58.091 50.000 25.47 7.61 44.48 2.57
2151 2273 5.560724 TCCACCTCAAATTTGGAGTAGAAG 58.439 41.667 17.90 6.13 34.35 2.85
2185 2307 7.444487 GGTACCTTTCTTGTCTCTTTGTATTGT 59.556 37.037 4.06 0.00 0.00 2.71
2189 2311 7.168135 CCTTTCTTGTCTCTTTGTATTGTTTGC 59.832 37.037 0.00 0.00 0.00 3.68
2192 2314 7.542890 TCTTGTCTCTTTGTATTGTTTGCAAA 58.457 30.769 8.05 8.05 37.55 3.68
2194 2316 6.862209 TGTCTCTTTGTATTGTTTGCAAACT 58.138 32.000 35.09 22.53 39.59 2.66
2195 2317 7.990917 TGTCTCTTTGTATTGTTTGCAAACTA 58.009 30.769 35.09 30.15 39.59 2.24
2197 2319 8.342634 GTCTCTTTGTATTGTTTGCAAACTAGA 58.657 33.333 35.09 25.78 39.59 2.43
2199 2321 9.121517 CTCTTTGTATTGTTTGCAAACTAGATG 57.878 33.333 35.09 20.07 39.59 2.90
2200 2322 8.845227 TCTTTGTATTGTTTGCAAACTAGATGA 58.155 29.630 35.09 21.54 39.59 2.92
2201 2323 8.795786 TTTGTATTGTTTGCAAACTAGATGAC 57.204 30.769 35.09 24.41 39.59 3.06
2202 2324 7.503521 TGTATTGTTTGCAAACTAGATGACA 57.496 32.000 35.09 26.08 39.59 3.58
2203 2325 7.935520 TGTATTGTTTGCAAACTAGATGACAA 58.064 30.769 35.09 23.01 39.59 3.18
2206 2328 5.771469 TGTTTGCAAACTAGATGACAATGG 58.229 37.500 35.09 0.00 39.59 3.16
2209 2331 5.375417 TGCAAACTAGATGACAATGGTTG 57.625 39.130 0.00 0.00 0.00 3.77
2215 2555 5.385198 ACTAGATGACAATGGTTGTTGGTT 58.615 37.500 0.00 0.00 45.52 3.67
2218 2558 5.630121 AGATGACAATGGTTGTTGGTTCTA 58.370 37.500 0.00 0.00 45.52 2.10
2219 2559 6.068010 AGATGACAATGGTTGTTGGTTCTAA 58.932 36.000 0.00 0.00 45.52 2.10
2226 2566 7.494298 ACAATGGTTGTTGGTTCTAATTTGTTC 59.506 33.333 0.00 0.00 42.22 3.18
2228 2568 6.936279 TGGTTGTTGGTTCTAATTTGTTCAA 58.064 32.000 0.00 0.00 0.00 2.69
2244 2584 9.991906 AATTTGTTCAAATTCTGAATGAGTGAT 57.008 25.926 15.08 0.00 45.74 3.06
2255 2595 8.442632 TTCTGAATGAGTGATATTCAATGTCC 57.557 34.615 0.00 0.00 42.21 4.02
2256 2596 7.799081 TCTGAATGAGTGATATTCAATGTCCT 58.201 34.615 0.00 0.00 42.21 3.85
2258 2598 9.551734 CTGAATGAGTGATATTCAATGTCCTAA 57.448 33.333 0.00 0.00 42.21 2.69
2303 2684 6.152492 TCACAGCAACATGGCTATTTTTATCA 59.848 34.615 0.00 0.00 43.68 2.15
2308 2689 7.707893 AGCAACATGGCTATTTTTATCATTCAC 59.292 33.333 0.00 0.00 43.70 3.18
2334 2716 7.867403 CACTTTTTATGAATCCGAATAATGGGG 59.133 37.037 0.00 0.00 0.00 4.96
2338 2720 4.351874 TGAATCCGAATAATGGGGTCTC 57.648 45.455 0.00 0.00 0.00 3.36
2339 2721 3.973973 TGAATCCGAATAATGGGGTCTCT 59.026 43.478 0.00 0.00 0.00 3.10
2358 2740 7.204604 GGTCTCTAGCTTCTCCTTGTATTTAC 58.795 42.308 0.00 0.00 0.00 2.01
2360 2742 6.039493 TCTCTAGCTTCTCCTTGTATTTACCG 59.961 42.308 0.00 0.00 0.00 4.02
2508 2891 7.193595 AGGTGTACAAGAACTTTCAAATTTCG 58.806 34.615 0.00 0.00 0.00 3.46
2670 3319 1.607628 CAAGCTATGGATTCAGGCAGC 59.392 52.381 4.82 1.49 0.00 5.25
2689 3338 4.367450 CAGCTAGACAGATTACAGGAAGC 58.633 47.826 0.00 0.00 0.00 3.86
2697 3346 2.012673 GATTACAGGAAGCTGCAGTGG 58.987 52.381 16.64 1.46 0.00 4.00
2716 3365 3.315470 GTGGTTTTCAGAGGGAAGAACAC 59.685 47.826 0.88 0.88 46.83 3.32
2765 3414 3.984633 GGCTCGAATCGAAGAATAGAAGG 59.015 47.826 6.84 0.00 43.58 3.46
2813 3462 1.573108 GATGGAGAGAGTTGGGGACA 58.427 55.000 0.00 0.00 39.83 4.02
2838 3487 0.171455 GCTTCAGATCTCACCGACGT 59.829 55.000 0.00 0.00 0.00 4.34
2864 3513 2.665000 CTCTCCTTGCCGCCTTCA 59.335 61.111 0.00 0.00 0.00 3.02
2929 3614 0.539669 CTGCCCCCGTTCTTTTTCCT 60.540 55.000 0.00 0.00 0.00 3.36
2958 3643 4.094442 GTCCCTCAAATACTTGGCTTAACG 59.906 45.833 0.00 0.00 33.01 3.18
3068 3753 1.043816 TGGATTTTGGCGCCTTTTCA 58.956 45.000 29.70 15.07 0.00 2.69
3097 3783 5.681639 ACCTACAAAAACAGAGTAGCACTT 58.318 37.500 0.00 0.00 35.15 3.16
3107 3793 5.420409 ACAGAGTAGCACTTTAACATAGCC 58.580 41.667 0.00 0.00 0.00 3.93
3136 3822 6.718454 GTGGCATTTTGTATGCAACATTTA 57.282 33.333 11.39 0.00 45.72 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.403323 TGAACAATTTGCGTGTGCTCA 59.597 42.857 0.00 0.00 43.34 4.26
5 6 2.118228 TGAACAATTTGCGTGTGCTC 57.882 45.000 0.00 0.00 43.34 4.26
6 7 2.396601 CATGAACAATTTGCGTGTGCT 58.603 42.857 0.00 0.00 43.34 4.40
7 8 1.456544 CCATGAACAATTTGCGTGTGC 59.543 47.619 0.00 0.00 43.20 4.57
8 9 1.456544 GCCATGAACAATTTGCGTGTG 59.543 47.619 0.00 0.00 0.00 3.82
9 10 1.340889 AGCCATGAACAATTTGCGTGT 59.659 42.857 0.00 0.00 0.00 4.49
10 11 1.722464 CAGCCATGAACAATTTGCGTG 59.278 47.619 0.00 0.00 0.00 5.34
11 12 1.936203 GCAGCCATGAACAATTTGCGT 60.936 47.619 0.00 0.00 0.00 5.24
12 13 0.717224 GCAGCCATGAACAATTTGCG 59.283 50.000 0.00 0.00 0.00 4.85
13 14 1.081094 GGCAGCCATGAACAATTTGC 58.919 50.000 6.55 0.00 0.00 3.68
14 15 2.343101 CAGGCAGCCATGAACAATTTG 58.657 47.619 15.80 0.00 0.00 2.32
15 16 1.276989 CCAGGCAGCCATGAACAATTT 59.723 47.619 15.80 0.00 0.00 1.82
16 17 0.899720 CCAGGCAGCCATGAACAATT 59.100 50.000 15.80 0.00 0.00 2.32
17 18 0.251922 ACCAGGCAGCCATGAACAAT 60.252 50.000 15.80 0.00 0.00 2.71
18 19 0.469705 AACCAGGCAGCCATGAACAA 60.470 50.000 15.80 0.00 0.00 2.83
19 20 0.469705 AAACCAGGCAGCCATGAACA 60.470 50.000 15.80 0.00 0.00 3.18
20 21 0.037975 CAAACCAGGCAGCCATGAAC 60.038 55.000 15.80 0.00 0.00 3.18
21 22 0.178967 TCAAACCAGGCAGCCATGAA 60.179 50.000 15.80 0.00 0.00 2.57
22 23 0.895100 GTCAAACCAGGCAGCCATGA 60.895 55.000 15.80 6.99 0.00 3.07
23 24 1.588082 GTCAAACCAGGCAGCCATG 59.412 57.895 15.80 9.03 0.00 3.66
24 25 1.607467 GGTCAAACCAGGCAGCCAT 60.607 57.895 15.80 0.00 38.42 4.40
25 26 2.203480 GGTCAAACCAGGCAGCCA 60.203 61.111 15.80 0.00 38.42 4.75
26 27 3.365265 CGGTCAAACCAGGCAGCC 61.365 66.667 1.84 1.84 38.47 4.85
27 28 1.648467 GATCGGTCAAACCAGGCAGC 61.648 60.000 0.00 0.00 38.47 5.25
28 29 1.026718 GGATCGGTCAAACCAGGCAG 61.027 60.000 0.00 0.00 38.47 4.85
29 30 1.002624 GGATCGGTCAAACCAGGCA 60.003 57.895 0.00 0.00 38.47 4.75
30 31 1.002624 TGGATCGGTCAAACCAGGC 60.003 57.895 0.00 0.00 38.47 4.85
31 32 0.613260 TCTGGATCGGTCAAACCAGG 59.387 55.000 0.00 0.00 46.64 4.45
33 34 3.433306 AATTCTGGATCGGTCAAACCA 57.567 42.857 0.00 0.00 38.47 3.67
34 35 4.275936 CCATAATTCTGGATCGGTCAAACC 59.724 45.833 3.79 0.00 38.69 3.27
35 36 5.007724 GTCCATAATTCTGGATCGGTCAAAC 59.992 44.000 15.00 0.00 46.67 2.93
36 37 5.123227 GTCCATAATTCTGGATCGGTCAAA 58.877 41.667 15.00 0.00 46.67 2.69
37 38 4.703897 GTCCATAATTCTGGATCGGTCAA 58.296 43.478 15.00 0.00 46.67 3.18
38 39 3.243737 CGTCCATAATTCTGGATCGGTCA 60.244 47.826 15.00 0.00 46.67 4.02
39 40 3.318017 CGTCCATAATTCTGGATCGGTC 58.682 50.000 15.00 2.28 46.67 4.79
40 41 2.548067 GCGTCCATAATTCTGGATCGGT 60.548 50.000 23.18 0.00 46.67 4.69
41 42 2.069273 GCGTCCATAATTCTGGATCGG 58.931 52.381 23.18 15.05 46.67 4.18
42 43 2.733552 CAGCGTCCATAATTCTGGATCG 59.266 50.000 15.00 18.28 46.67 3.69
43 44 3.733337 ACAGCGTCCATAATTCTGGATC 58.267 45.455 15.00 10.36 46.67 3.36
44 45 3.845781 ACAGCGTCCATAATTCTGGAT 57.154 42.857 15.00 0.00 46.67 3.41
45 46 3.270027 CAACAGCGTCCATAATTCTGGA 58.730 45.455 8.43 8.43 43.09 3.86
46 47 2.355756 CCAACAGCGTCCATAATTCTGG 59.644 50.000 3.46 3.46 37.66 3.86
47 48 3.009723 ACCAACAGCGTCCATAATTCTG 58.990 45.455 0.00 0.00 0.00 3.02
48 49 3.350219 ACCAACAGCGTCCATAATTCT 57.650 42.857 0.00 0.00 0.00 2.40
49 50 3.689649 AGAACCAACAGCGTCCATAATTC 59.310 43.478 0.00 0.00 0.00 2.17
50 51 3.440173 CAGAACCAACAGCGTCCATAATT 59.560 43.478 0.00 0.00 0.00 1.40
51 52 3.009723 CAGAACCAACAGCGTCCATAAT 58.990 45.455 0.00 0.00 0.00 1.28
52 53 2.037902 TCAGAACCAACAGCGTCCATAA 59.962 45.455 0.00 0.00 0.00 1.90
53 54 1.621317 TCAGAACCAACAGCGTCCATA 59.379 47.619 0.00 0.00 0.00 2.74
54 55 0.396435 TCAGAACCAACAGCGTCCAT 59.604 50.000 0.00 0.00 0.00 3.41
55 56 0.179234 TTCAGAACCAACAGCGTCCA 59.821 50.000 0.00 0.00 0.00 4.02
56 57 0.586802 GTTCAGAACCAACAGCGTCC 59.413 55.000 1.29 0.00 0.00 4.79
67 68 2.765135 GTCCCCTACCTAGGTTCAGAAC 59.235 54.545 22.11 9.97 42.03 3.01
68 69 2.384375 TGTCCCCTACCTAGGTTCAGAA 59.616 50.000 22.11 0.00 42.03 3.02
69 70 2.005350 TGTCCCCTACCTAGGTTCAGA 58.995 52.381 22.11 9.53 42.03 3.27
70 71 2.544844 TGTCCCCTACCTAGGTTCAG 57.455 55.000 22.11 12.43 42.03 3.02
71 72 2.045326 ACATGTCCCCTACCTAGGTTCA 59.955 50.000 22.11 10.33 42.03 3.18
72 73 2.760581 ACATGTCCCCTACCTAGGTTC 58.239 52.381 22.11 5.02 42.03 3.62
73 74 2.963654 ACATGTCCCCTACCTAGGTT 57.036 50.000 22.11 4.29 42.03 3.50
74 75 3.274153 ACTTACATGTCCCCTACCTAGGT 59.726 47.826 20.57 20.57 42.03 3.08
75 76 3.924922 ACTTACATGTCCCCTACCTAGG 58.075 50.000 7.41 7.41 43.25 3.02
76 77 4.523558 GCTACTTACATGTCCCCTACCTAG 59.476 50.000 0.00 0.00 0.00 3.02
77 78 4.169461 AGCTACTTACATGTCCCCTACCTA 59.831 45.833 0.00 0.00 0.00 3.08
78 79 3.052033 AGCTACTTACATGTCCCCTACCT 60.052 47.826 0.00 0.00 0.00 3.08
79 80 3.306613 AGCTACTTACATGTCCCCTACC 58.693 50.000 0.00 0.00 0.00 3.18
80 81 5.139001 ACTAGCTACTTACATGTCCCCTAC 58.861 45.833 0.00 0.00 0.00 3.18
81 82 5.103813 TGACTAGCTACTTACATGTCCCCTA 60.104 44.000 0.00 0.00 0.00 3.53
82 83 4.216708 GACTAGCTACTTACATGTCCCCT 58.783 47.826 0.00 0.00 0.00 4.79
83 84 3.958798 TGACTAGCTACTTACATGTCCCC 59.041 47.826 0.00 0.00 0.00 4.81
84 85 5.593679 TTGACTAGCTACTTACATGTCCC 57.406 43.478 0.00 0.00 0.00 4.46
85 86 7.382759 GCTAATTGACTAGCTACTTACATGTCC 59.617 40.741 0.00 0.00 41.01 4.02
86 87 7.382759 GGCTAATTGACTAGCTACTTACATGTC 59.617 40.741 0.00 0.00 43.28 3.06
87 88 7.210873 GGCTAATTGACTAGCTACTTACATGT 58.789 38.462 2.69 2.69 43.28 3.21
88 89 6.647067 GGGCTAATTGACTAGCTACTTACATG 59.353 42.308 2.89 0.00 43.28 3.21
89 90 6.239629 GGGGCTAATTGACTAGCTACTTACAT 60.240 42.308 2.89 0.00 43.28 2.29
90 91 5.070047 GGGGCTAATTGACTAGCTACTTACA 59.930 44.000 2.89 0.00 43.28 2.41
91 92 5.304871 AGGGGCTAATTGACTAGCTACTTAC 59.695 44.000 2.89 0.00 43.28 2.34
92 93 5.464984 AGGGGCTAATTGACTAGCTACTTA 58.535 41.667 2.89 0.00 43.28 2.24
93 94 4.299485 AGGGGCTAATTGACTAGCTACTT 58.701 43.478 2.89 0.00 43.28 2.24
94 95 3.930035 AGGGGCTAATTGACTAGCTACT 58.070 45.455 2.89 0.00 43.28 2.57
95 96 4.691326 AAGGGGCTAATTGACTAGCTAC 57.309 45.455 2.89 0.00 43.28 3.58
96 97 4.686122 GCAAAGGGGCTAATTGACTAGCTA 60.686 45.833 0.00 0.00 43.28 3.32
97 98 3.891049 CAAAGGGGCTAATTGACTAGCT 58.109 45.455 0.00 0.00 43.28 3.32
98 99 2.359214 GCAAAGGGGCTAATTGACTAGC 59.641 50.000 0.00 0.00 43.06 3.42
99 100 3.629398 CAGCAAAGGGGCTAATTGACTAG 59.371 47.826 0.00 0.00 43.68 2.57
100 101 3.620488 CAGCAAAGGGGCTAATTGACTA 58.380 45.455 0.00 0.00 43.68 2.59
101 102 2.450476 CAGCAAAGGGGCTAATTGACT 58.550 47.619 0.00 0.00 43.68 3.41
102 103 1.134995 GCAGCAAAGGGGCTAATTGAC 60.135 52.381 0.00 0.00 43.68 3.18
103 104 1.185315 GCAGCAAAGGGGCTAATTGA 58.815 50.000 0.00 0.00 43.68 2.57
104 105 0.176449 GGCAGCAAAGGGGCTAATTG 59.824 55.000 0.00 0.00 43.68 2.32
105 106 1.322538 CGGCAGCAAAGGGGCTAATT 61.323 55.000 0.00 0.00 43.68 1.40
106 107 1.754234 CGGCAGCAAAGGGGCTAAT 60.754 57.895 0.00 0.00 43.68 1.73
107 108 2.361104 CGGCAGCAAAGGGGCTAA 60.361 61.111 0.00 0.00 43.68 3.09
108 109 4.424711 CCGGCAGCAAAGGGGCTA 62.425 66.667 0.00 0.00 43.68 3.93
118 119 1.026718 AGATAAACTGTGCCGGCAGC 61.027 55.000 33.73 24.46 39.96 5.25
119 120 2.205074 CTAGATAAACTGTGCCGGCAG 58.795 52.381 33.73 22.63 41.92 4.85
120 121 1.742411 GCTAGATAAACTGTGCCGGCA 60.742 52.381 29.03 29.03 0.00 5.69
121 122 0.938008 GCTAGATAAACTGTGCCGGC 59.062 55.000 22.73 22.73 0.00 6.13
122 123 2.309528 TGCTAGATAAACTGTGCCGG 57.690 50.000 0.00 0.00 0.00 6.13
123 124 4.882671 ATTTGCTAGATAAACTGTGCCG 57.117 40.909 0.00 0.00 0.00 5.69
124 125 8.026607 TGTTTAATTTGCTAGATAAACTGTGCC 58.973 33.333 14.20 0.00 38.46 5.01
125 126 8.850452 GTGTTTAATTTGCTAGATAAACTGTGC 58.150 33.333 14.20 0.00 38.46 4.57
126 127 9.891828 TGTGTTTAATTTGCTAGATAAACTGTG 57.108 29.630 14.20 0.00 38.46 3.66
147 148 9.319143 GCTCACTCATAAATTCTAGTATGTGTT 57.681 33.333 4.09 0.00 34.07 3.32
148 149 8.478066 TGCTCACTCATAAATTCTAGTATGTGT 58.522 33.333 0.00 0.00 35.75 3.72
149 150 8.877808 TGCTCACTCATAAATTCTAGTATGTG 57.122 34.615 0.00 0.00 0.00 3.21
150 151 9.319143 GTTGCTCACTCATAAATTCTAGTATGT 57.681 33.333 0.00 0.00 0.00 2.29
151 152 9.317936 TGTTGCTCACTCATAAATTCTAGTATG 57.682 33.333 0.00 0.00 0.00 2.39
152 153 9.539825 CTGTTGCTCACTCATAAATTCTAGTAT 57.460 33.333 0.00 0.00 0.00 2.12
153 154 8.749354 TCTGTTGCTCACTCATAAATTCTAGTA 58.251 33.333 0.00 0.00 0.00 1.82
154 155 7.615403 TCTGTTGCTCACTCATAAATTCTAGT 58.385 34.615 0.00 0.00 0.00 2.57
155 156 8.549548 CATCTGTTGCTCACTCATAAATTCTAG 58.450 37.037 0.00 0.00 0.00 2.43
156 157 7.496920 CCATCTGTTGCTCACTCATAAATTCTA 59.503 37.037 0.00 0.00 0.00 2.10
157 158 6.318144 CCATCTGTTGCTCACTCATAAATTCT 59.682 38.462 0.00 0.00 0.00 2.40
158 159 6.459298 CCCATCTGTTGCTCACTCATAAATTC 60.459 42.308 0.00 0.00 0.00 2.17
159 160 5.359009 CCCATCTGTTGCTCACTCATAAATT 59.641 40.000 0.00 0.00 0.00 1.82
160 161 4.885907 CCCATCTGTTGCTCACTCATAAAT 59.114 41.667 0.00 0.00 0.00 1.40
161 162 4.264253 CCCATCTGTTGCTCACTCATAAA 58.736 43.478 0.00 0.00 0.00 1.40
162 163 3.877559 CCCATCTGTTGCTCACTCATAA 58.122 45.455 0.00 0.00 0.00 1.90
163 164 2.420547 GCCCATCTGTTGCTCACTCATA 60.421 50.000 0.00 0.00 0.00 2.15
164 165 1.681166 GCCCATCTGTTGCTCACTCAT 60.681 52.381 0.00 0.00 0.00 2.90
165 166 0.321919 GCCCATCTGTTGCTCACTCA 60.322 55.000 0.00 0.00 0.00 3.41
166 167 0.321919 TGCCCATCTGTTGCTCACTC 60.322 55.000 0.00 0.00 0.00 3.51
167 168 0.111061 TTGCCCATCTGTTGCTCACT 59.889 50.000 0.00 0.00 0.00 3.41
168 169 0.961019 TTTGCCCATCTGTTGCTCAC 59.039 50.000 0.00 0.00 0.00 3.51
169 170 1.614903 CTTTTGCCCATCTGTTGCTCA 59.385 47.619 0.00 0.00 0.00 4.26
170 171 1.888512 TCTTTTGCCCATCTGTTGCTC 59.111 47.619 0.00 0.00 0.00 4.26
171 172 1.999648 TCTTTTGCCCATCTGTTGCT 58.000 45.000 0.00 0.00 0.00 3.91
172 173 2.224018 TGTTCTTTTGCCCATCTGTTGC 60.224 45.455 0.00 0.00 0.00 4.17
173 174 3.731652 TGTTCTTTTGCCCATCTGTTG 57.268 42.857 0.00 0.00 0.00 3.33
174 175 3.896888 TGATGTTCTTTTGCCCATCTGTT 59.103 39.130 0.00 0.00 35.76 3.16
175 176 3.499338 TGATGTTCTTTTGCCCATCTGT 58.501 40.909 0.00 0.00 35.76 3.41
176 177 3.675228 GCTGATGTTCTTTTGCCCATCTG 60.675 47.826 0.00 0.00 35.76 2.90
177 178 2.494870 GCTGATGTTCTTTTGCCCATCT 59.505 45.455 0.00 0.00 35.76 2.90
178 179 2.494870 AGCTGATGTTCTTTTGCCCATC 59.505 45.455 0.00 0.00 35.40 3.51
179 180 2.494870 GAGCTGATGTTCTTTTGCCCAT 59.505 45.455 0.00 0.00 0.00 4.00
180 181 1.888512 GAGCTGATGTTCTTTTGCCCA 59.111 47.619 0.00 0.00 0.00 5.36
181 182 1.888512 TGAGCTGATGTTCTTTTGCCC 59.111 47.619 0.00 0.00 0.00 5.36
182 183 3.863142 ATGAGCTGATGTTCTTTTGCC 57.137 42.857 0.00 0.00 0.00 4.52
183 184 6.666417 CCTATATGAGCTGATGTTCTTTTGC 58.334 40.000 0.00 0.00 0.00 3.68
184 185 6.261603 TGCCTATATGAGCTGATGTTCTTTTG 59.738 38.462 0.00 0.00 0.00 2.44
185 186 6.261826 GTGCCTATATGAGCTGATGTTCTTTT 59.738 38.462 0.00 0.00 0.00 2.27
186 187 5.762218 GTGCCTATATGAGCTGATGTTCTTT 59.238 40.000 0.00 0.00 0.00 2.52
187 188 5.071519 AGTGCCTATATGAGCTGATGTTCTT 59.928 40.000 0.00 0.00 0.00 2.52
188 189 4.592351 AGTGCCTATATGAGCTGATGTTCT 59.408 41.667 0.00 0.00 0.00 3.01
189 190 4.892433 AGTGCCTATATGAGCTGATGTTC 58.108 43.478 0.00 0.00 0.00 3.18
190 191 4.970860 AGTGCCTATATGAGCTGATGTT 57.029 40.909 0.00 0.00 0.00 2.71
191 192 4.102210 ACAAGTGCCTATATGAGCTGATGT 59.898 41.667 0.00 0.00 0.00 3.06
192 193 4.451435 CACAAGTGCCTATATGAGCTGATG 59.549 45.833 0.00 0.71 0.00 3.07
193 194 4.102210 ACACAAGTGCCTATATGAGCTGAT 59.898 41.667 0.00 0.00 0.00 2.90
194 195 3.452264 ACACAAGTGCCTATATGAGCTGA 59.548 43.478 0.00 0.00 0.00 4.26
195 196 3.558829 CACACAAGTGCCTATATGAGCTG 59.441 47.826 0.00 0.00 39.21 4.24
196 197 3.432749 CCACACAAGTGCCTATATGAGCT 60.433 47.826 0.00 0.00 44.53 4.09
197 198 2.874701 CCACACAAGTGCCTATATGAGC 59.125 50.000 0.00 0.00 44.53 4.26
198 199 3.873361 CACCACACAAGTGCCTATATGAG 59.127 47.826 0.00 0.00 44.53 2.90
237 238 2.335011 GGCAGTTTGGTTCACGGC 59.665 61.111 0.00 0.00 34.90 5.68
238 239 2.637025 CGGCAGTTTGGTTCACGG 59.363 61.111 0.00 0.00 0.00 4.94
253 254 2.633657 GTAATGGCGATGCAGCGG 59.366 61.111 27.22 8.00 38.18 5.52
303 309 8.574737 AGAGTTTCAGAATTCAGATTTTTCAGG 58.425 33.333 8.44 0.00 0.00 3.86
338 344 2.806945 ACTCTACTCTGCTCTGCTCT 57.193 50.000 0.00 0.00 0.00 4.09
339 345 3.804036 TCTACTCTACTCTGCTCTGCTC 58.196 50.000 0.00 0.00 0.00 4.26
340 346 3.199946 ACTCTACTCTACTCTGCTCTGCT 59.800 47.826 0.00 0.00 0.00 4.24
341 347 3.541632 ACTCTACTCTACTCTGCTCTGC 58.458 50.000 0.00 0.00 0.00 4.26
342 348 6.156748 TCTACTCTACTCTACTCTGCTCTG 57.843 45.833 0.00 0.00 0.00 3.35
343 349 5.221461 GCTCTACTCTACTCTACTCTGCTCT 60.221 48.000 0.00 0.00 0.00 4.09
344 350 4.989168 GCTCTACTCTACTCTACTCTGCTC 59.011 50.000 0.00 0.00 0.00 4.26
345 351 4.654262 AGCTCTACTCTACTCTACTCTGCT 59.346 45.833 0.00 0.00 0.00 4.24
346 352 4.750098 CAGCTCTACTCTACTCTACTCTGC 59.250 50.000 0.00 0.00 0.00 4.26
347 353 5.297547 CCAGCTCTACTCTACTCTACTCTG 58.702 50.000 0.00 0.00 0.00 3.35
348 354 4.202326 GCCAGCTCTACTCTACTCTACTCT 60.202 50.000 0.00 0.00 0.00 3.24
349 355 4.062991 GCCAGCTCTACTCTACTCTACTC 58.937 52.174 0.00 0.00 0.00 2.59
350 356 3.714798 AGCCAGCTCTACTCTACTCTACT 59.285 47.826 0.00 0.00 0.00 2.57
351 357 4.062991 GAGCCAGCTCTACTCTACTCTAC 58.937 52.174 12.42 0.00 39.80 2.59
352 358 3.712218 TGAGCCAGCTCTACTCTACTCTA 59.288 47.826 19.71 0.00 43.12 2.43
411 418 3.881089 CCATATCACTCTGCATTGCTTGA 59.119 43.478 10.49 7.59 0.00 3.02
415 422 4.155462 CCATACCATATCACTCTGCATTGC 59.845 45.833 0.46 0.46 0.00 3.56
476 491 3.248024 TCCCCTTGTAGCTTCAGAAAGA 58.752 45.455 0.00 0.00 34.14 2.52
504 523 6.580416 GTCGACAAGAAAGGTACTAACTACAC 59.420 42.308 11.55 0.00 38.49 2.90
509 528 3.363128 GCGTCGACAAGAAAGGTACTAAC 59.637 47.826 17.16 0.00 38.49 2.34
510 529 3.004629 TGCGTCGACAAGAAAGGTACTAA 59.995 43.478 17.16 0.00 38.49 2.24
511 530 2.553602 TGCGTCGACAAGAAAGGTACTA 59.446 45.455 17.16 0.00 38.49 1.82
662 697 5.782331 TCCCCTGATCCAGTAGATATCTTTG 59.218 44.000 11.25 9.87 34.42 2.77
668 714 3.076182 GTCCTCCCCTGATCCAGTAGATA 59.924 52.174 0.00 0.00 34.42 1.98
672 718 0.106167 CGTCCTCCCCTGATCCAGTA 60.106 60.000 0.00 0.00 0.00 2.74
785 866 4.103103 TGCTCGTCGTGCTCCTCG 62.103 66.667 18.94 0.00 0.00 4.63
847 937 4.424711 TGGCCCGTCCAGCAATCC 62.425 66.667 0.00 0.00 40.72 3.01
1071 1193 3.213402 CGGAGGGAGAGGAGCGTC 61.213 72.222 0.00 0.00 0.00 5.19
1263 1385 4.988716 TCGAGGGTGGCCGTGACT 62.989 66.667 0.00 0.00 0.00 3.41
1315 1437 3.399181 GGACGGGGAGGTGATGCA 61.399 66.667 0.00 0.00 0.00 3.96
1638 1760 1.815421 GCTCCGCACCATGACGAAT 60.815 57.895 0.00 0.00 0.00 3.34
1662 1784 2.432628 GACACGAGGCAGAACGGG 60.433 66.667 0.00 0.00 38.94 5.28
1770 1892 1.729881 GCCCATGGCGATGTTCTTC 59.270 57.895 6.09 0.00 39.62 2.87
1998 2120 1.202330 CCTCTCCCTCAATGACAGCT 58.798 55.000 0.00 0.00 0.00 4.24
2151 2273 4.707934 AGACAAGAAAGGTACCTCTCTAGC 59.292 45.833 18.28 10.35 0.00 3.42
2185 2307 6.183360 ACAACCATTGTCATCTAGTTTGCAAA 60.183 34.615 8.05 8.05 40.56 3.68
2189 2311 6.151691 CCAACAACCATTGTCATCTAGTTTG 58.848 40.000 0.00 0.00 44.59 2.93
2192 2314 4.985538 ACCAACAACCATTGTCATCTAGT 58.014 39.130 0.00 0.00 44.59 2.57
2194 2316 5.630121 AGAACCAACAACCATTGTCATCTA 58.370 37.500 0.00 0.00 44.59 1.98
2195 2317 4.473444 AGAACCAACAACCATTGTCATCT 58.527 39.130 0.00 0.00 44.59 2.90
2197 2319 6.916360 ATTAGAACCAACAACCATTGTCAT 57.084 33.333 0.00 0.00 44.59 3.06
2199 2321 6.983890 ACAAATTAGAACCAACAACCATTGTC 59.016 34.615 0.00 0.00 44.59 3.18
2201 2323 7.493971 TGAACAAATTAGAACCAACAACCATTG 59.506 33.333 0.00 0.00 0.00 2.82
2202 2324 7.560368 TGAACAAATTAGAACCAACAACCATT 58.440 30.769 0.00 0.00 0.00 3.16
2203 2325 7.118496 TGAACAAATTAGAACCAACAACCAT 57.882 32.000 0.00 0.00 0.00 3.55
2244 2584 8.956426 GTCCAAGACAAATTAGGACATTGAATA 58.044 33.333 0.00 0.00 46.15 1.75
2246 2586 7.214467 GTCCAAGACAAATTAGGACATTGAA 57.786 36.000 0.00 0.00 46.15 2.69
2247 2587 6.817765 GTCCAAGACAAATTAGGACATTGA 57.182 37.500 0.00 0.00 46.15 2.57
2252 2592 4.072131 TGCTGTCCAAGACAAATTAGGAC 58.928 43.478 0.00 0.00 46.86 3.85
2253 2593 4.326826 CTGCTGTCCAAGACAAATTAGGA 58.673 43.478 0.00 0.00 42.26 2.94
2254 2594 3.119708 GCTGCTGTCCAAGACAAATTAGG 60.120 47.826 0.00 0.00 42.26 2.69
2255 2595 3.755378 AGCTGCTGTCCAAGACAAATTAG 59.245 43.478 0.00 0.00 42.26 1.73
2256 2596 3.754965 AGCTGCTGTCCAAGACAAATTA 58.245 40.909 0.00 0.00 42.26 1.40
2258 2598 2.283145 AGCTGCTGTCCAAGACAAAT 57.717 45.000 0.00 0.00 42.26 2.32
2259 2599 1.949525 GAAGCTGCTGTCCAAGACAAA 59.050 47.619 1.35 0.00 42.26 2.83
2308 2689 7.867403 CCCCATTATTCGGATTCATAAAAAGTG 59.133 37.037 0.00 0.00 0.00 3.16
2324 2705 5.279758 GGAGAAGCTAGAGACCCCATTATTC 60.280 48.000 0.00 0.00 0.00 1.75
2334 2716 7.204604 GGTAAATACAAGGAGAAGCTAGAGAC 58.795 42.308 0.00 0.00 0.00 3.36
2338 2720 5.903810 ACGGTAAATACAAGGAGAAGCTAG 58.096 41.667 0.00 0.00 0.00 3.42
2339 2721 5.927281 ACGGTAAATACAAGGAGAAGCTA 57.073 39.130 0.00 0.00 0.00 3.32
2358 2740 2.665649 TGGCATAGTGTTCACTACGG 57.334 50.000 13.78 10.65 0.00 4.02
2360 2742 6.743575 AGAAAATGGCATAGTGTTCACTAC 57.256 37.500 13.78 4.00 0.00 2.73
2394 2776 1.202290 ACAACTTGCAGCAAAACCTCG 60.202 47.619 9.65 0.00 0.00 4.63
2508 2891 5.619625 ATCTTCAAACTCTACTGCTTTGC 57.380 39.130 0.00 0.00 0.00 3.68
2602 3109 4.295870 CTGTGTTTGTTACTGCTCGTCTA 58.704 43.478 0.00 0.00 0.00 2.59
2670 3319 4.142071 TGCAGCTTCCTGTAATCTGTCTAG 60.142 45.833 0.00 0.00 41.26 2.43
2689 3338 1.202806 TCCCTCTGAAAACCACTGCAG 60.203 52.381 13.48 13.48 0.00 4.41
2697 3346 4.881850 TGAAGTGTTCTTCCCTCTGAAAAC 59.118 41.667 5.68 0.00 46.66 2.43
2716 3365 7.434492 TCAACCTGTAAGACTAAGTTCTGAAG 58.566 38.462 0.00 0.00 34.07 3.02
2765 3414 3.222603 TCTCCTTCAAAGTTCAAAGCCC 58.777 45.455 0.00 0.00 0.00 5.19
2813 3462 2.672478 CGGTGAGATCTGAAGCGAGTTT 60.672 50.000 17.44 0.00 36.98 2.66
2838 3487 1.330655 GGCAAGGAGAGGACGATGGA 61.331 60.000 0.00 0.00 0.00 3.41
2864 3513 3.257127 CAGAACGAGAGAAAAGAGGGAGT 59.743 47.826 0.00 0.00 0.00 3.85
2894 3543 3.505386 GGGCAGAGATCAGATAAGGAGA 58.495 50.000 0.00 0.00 0.00 3.71
2900 3584 0.188587 ACGGGGGCAGAGATCAGATA 59.811 55.000 0.00 0.00 0.00 1.98
2929 3614 5.007682 GCCAAGTATTTGAGGGACTAAACA 58.992 41.667 0.00 0.00 41.55 2.83
2958 3643 1.064654 GAATGAGGGAACATCTTGCGC 59.935 52.381 0.00 0.00 0.00 6.09
3068 3753 3.692593 ACTCTGTTTTTGTAGGTTTGCGT 59.307 39.130 0.00 0.00 0.00 5.24
3107 3793 2.411409 GCATACAAAATGCCACAAACGG 59.589 45.455 0.00 0.00 39.01 4.44


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

AutoCloner maintained by Alex Coulton.