Multiple sequence alignment - TraesCS6A01G225300

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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 TraesCS6A01G225300 chr6A 100.000 4620 0 0 1 4620 423525570 423520951 0.000000e+00 8532.0
1 TraesCS6A01G225300 chr6A 82.064 1037 155 26 2409 3431 423534280 423533261 0.000000e+00 856.0
2 TraesCS6A01G225300 chr6A 81.627 664 109 11 3877 4533 448021313 448020656 5.260000e-149 538.0
3 TraesCS6A01G225300 chr6A 79.518 581 108 10 3974 4549 589077786 589077212 2.000000e-108 403.0
4 TraesCS6A01G225300 chr6A 79.182 538 98 13 4018 4549 462266903 462267432 1.220000e-95 361.0
5 TraesCS6A01G225300 chr6D 93.428 4489 184 44 201 4620 296755256 296750810 0.000000e+00 6553.0
6 TraesCS6A01G225300 chr6D 81.678 1037 153 31 2409 3431 296825249 296824236 0.000000e+00 828.0
7 TraesCS6A01G225300 chr6D 74.247 897 181 35 1197 2062 296826543 296825666 9.580000e-87 331.0
8 TraesCS6A01G225300 chr6D 78.395 486 91 13 4069 4549 298063191 298063667 2.090000e-78 303.0
9 TraesCS6A01G225300 chr6B 94.629 3426 124 29 746 4131 460274053 460277458 0.000000e+00 5252.0
10 TraesCS6A01G225300 chr6B 90.436 711 60 7 3904 4612 460279449 460280153 0.000000e+00 929.0
11 TraesCS6A01G225300 chr6B 81.808 874 116 27 2409 3263 460209078 460209927 0.000000e+00 693.0
12 TraesCS6A01G225300 chr6B 89.516 496 28 4 195 685 460273562 460274038 1.420000e-169 606.0
13 TraesCS6A01G225300 chr5B 78.609 963 162 29 2494 3431 115418576 115419519 8.560000e-167 597.0
14 TraesCS6A01G225300 chr5B 80.389 566 97 13 3970 4527 153298603 153299162 7.150000e-113 418.0
15 TraesCS6A01G225300 chr5B 94.231 52 3 0 3817 3868 625122715 625122664 3.830000e-11 80.5
16 TraesCS6A01G225300 chr5B 94.231 52 3 0 3817 3868 628702265 628702214 3.830000e-11 80.5
17 TraesCS6A01G225300 chr5B 92.308 52 4 0 3817 3868 629918330 629918279 1.780000e-09 75.0
18 TraesCS6A01G225300 chr1D 80.354 621 101 16 3877 4490 344202904 344202298 7.050000e-123 451.0
19 TraesCS6A01G225300 chr3D 78.592 696 129 18 3876 4562 254215935 254216619 4.240000e-120 442.0
20 TraesCS6A01G225300 chr3D 90.991 111 9 1 3876 3986 254215627 254215736 1.040000e-31 148.0
21 TraesCS6A01G225300 chr5D 74.359 273 41 22 2955 3208 72902576 72902314 6.370000e-14 89.8
22 TraesCS6A01G225300 chr4D 80.508 118 21 2 3104 3220 401077133 401077017 6.370000e-14 89.8
23 TraesCS6A01G225300 chr4A 72.542 295 69 10 2935 3220 58869629 58869338 8.240000e-13 86.1
24 TraesCS6A01G225300 chr4B 72.542 295 67 12 2935 3219 495584559 495584269 2.960000e-12 84.2
25 TraesCS6A01G225300 chr3A 94.545 55 2 1 3814 3868 709156628 709156681 2.960000e-12 84.2
26 TraesCS6A01G225300 chr7B 92.453 53 4 0 3816 3868 154365075 154365023 4.960000e-10 76.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G225300 chr6A 423520951 423525570 4619 True 8532.000000 8532 100.0000 1 4620 1 chr6A.!!$R1 4619
1 TraesCS6A01G225300 chr6A 423533261 423534280 1019 True 856.000000 856 82.0640 2409 3431 1 chr6A.!!$R2 1022
2 TraesCS6A01G225300 chr6A 448020656 448021313 657 True 538.000000 538 81.6270 3877 4533 1 chr6A.!!$R3 656
3 TraesCS6A01G225300 chr6A 589077212 589077786 574 True 403.000000 403 79.5180 3974 4549 1 chr6A.!!$R4 575
4 TraesCS6A01G225300 chr6A 462266903 462267432 529 False 361.000000 361 79.1820 4018 4549 1 chr6A.!!$F1 531
5 TraesCS6A01G225300 chr6D 296750810 296755256 4446 True 6553.000000 6553 93.4280 201 4620 1 chr6D.!!$R1 4419
6 TraesCS6A01G225300 chr6D 296824236 296826543 2307 True 579.500000 828 77.9625 1197 3431 2 chr6D.!!$R2 2234
7 TraesCS6A01G225300 chr6B 460273562 460280153 6591 False 2262.333333 5252 91.5270 195 4612 3 chr6B.!!$F2 4417
8 TraesCS6A01G225300 chr6B 460209078 460209927 849 False 693.000000 693 81.8080 2409 3263 1 chr6B.!!$F1 854
9 TraesCS6A01G225300 chr5B 115418576 115419519 943 False 597.000000 597 78.6090 2494 3431 1 chr5B.!!$F1 937
10 TraesCS6A01G225300 chr5B 153298603 153299162 559 False 418.000000 418 80.3890 3970 4527 1 chr5B.!!$F2 557
11 TraesCS6A01G225300 chr1D 344202298 344202904 606 True 451.000000 451 80.3540 3877 4490 1 chr1D.!!$R1 613
12 TraesCS6A01G225300 chr3D 254215627 254216619 992 False 295.000000 442 84.7915 3876 4562 2 chr3D.!!$F1 686

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
177 178 0.033504 GCCGTTCTCCTTGTGACTGA 59.966 55.0 0.00 0.0 0.0 3.41 F
347 348 0.036765 ATGAGGACTTTGCGGCGTTA 60.037 50.0 9.37 0.0 0.0 3.18 F
1095 1130 0.468648 GATTAACACTCCCCCTCCGG 59.531 60.0 0.00 0.0 0.0 5.14 F
2100 2184 0.249447 GGTTGCTTGTTTCCACTGCC 60.249 55.0 0.00 0.0 0.0 4.85 F
3024 3208 0.454600 TCCAACATACTCCTCGACGC 59.545 55.0 0.00 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1100 1135 0.035056 GGAATGGGATAGGATGGCCG 60.035 60.000 0.00 0.00 39.96 6.13 R
2100 2184 0.439985 CACCATGAAGTGAACTCGCG 59.560 55.000 0.00 0.00 40.34 5.87 R
2145 2229 1.035385 TATCTGCGAGGACAAGGCGA 61.035 55.000 0.00 0.00 0.00 5.54 R
3472 3665 0.249657 CCACTAGCTCCGCAGAATCC 60.250 60.000 0.00 0.00 0.00 3.01 R
4522 7266 1.202818 GGTGGAGGTATCCTTGGATGC 60.203 57.143 12.08 10.43 46.80 3.91 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
18 19 3.612517 TCTCAGTGCGCACAAGATT 57.387 47.368 39.21 18.32 0.00 2.40
19 20 1.432514 TCTCAGTGCGCACAAGATTC 58.567 50.000 39.21 13.68 0.00 2.52
20 21 1.150827 CTCAGTGCGCACAAGATTCA 58.849 50.000 39.21 15.81 0.00 2.57
21 22 1.532437 CTCAGTGCGCACAAGATTCAA 59.468 47.619 39.21 15.47 0.00 2.69
22 23 1.946081 TCAGTGCGCACAAGATTCAAA 59.054 42.857 39.21 13.50 0.00 2.69
23 24 2.031769 TCAGTGCGCACAAGATTCAAAG 60.032 45.455 39.21 16.26 0.00 2.77
24 25 1.267806 AGTGCGCACAAGATTCAAAGG 59.732 47.619 39.21 0.00 0.00 3.11
25 26 1.266718 GTGCGCACAAGATTCAAAGGA 59.733 47.619 34.52 0.00 0.00 3.36
26 27 2.095059 GTGCGCACAAGATTCAAAGGAT 60.095 45.455 34.52 0.00 0.00 3.24
27 28 2.557924 TGCGCACAAGATTCAAAGGATT 59.442 40.909 5.66 0.00 0.00 3.01
28 29 3.174375 GCGCACAAGATTCAAAGGATTC 58.826 45.455 0.30 0.00 0.00 2.52
29 30 3.119708 GCGCACAAGATTCAAAGGATTCT 60.120 43.478 0.30 0.00 35.76 2.40
30 31 4.094887 GCGCACAAGATTCAAAGGATTCTA 59.905 41.667 0.30 0.00 33.73 2.10
31 32 5.728898 GCGCACAAGATTCAAAGGATTCTAG 60.729 44.000 0.30 0.00 33.73 2.43
32 33 5.220739 CGCACAAGATTCAAAGGATTCTAGG 60.221 44.000 0.00 0.00 33.73 3.02
33 34 5.649831 GCACAAGATTCAAAGGATTCTAGGT 59.350 40.000 0.00 0.00 33.73 3.08
34 35 6.823689 GCACAAGATTCAAAGGATTCTAGGTA 59.176 38.462 0.00 0.00 33.73 3.08
35 36 7.336931 GCACAAGATTCAAAGGATTCTAGGTAA 59.663 37.037 0.00 0.00 33.73 2.85
36 37 9.231297 CACAAGATTCAAAGGATTCTAGGTAAA 57.769 33.333 0.00 0.00 33.73 2.01
37 38 9.454859 ACAAGATTCAAAGGATTCTAGGTAAAG 57.545 33.333 0.00 0.00 33.73 1.85
38 39 9.672673 CAAGATTCAAAGGATTCTAGGTAAAGA 57.327 33.333 0.00 0.00 33.73 2.52
43 44 8.807948 TCAAAGGATTCTAGGTAAAGAAATGG 57.192 34.615 0.00 0.00 38.90 3.16
44 45 8.390921 TCAAAGGATTCTAGGTAAAGAAATGGT 58.609 33.333 0.00 0.00 38.90 3.55
45 46 9.681062 CAAAGGATTCTAGGTAAAGAAATGGTA 57.319 33.333 0.00 0.00 38.90 3.25
48 49 9.682465 AGGATTCTAGGTAAAGAAATGGTAAAC 57.318 33.333 0.00 0.00 38.90 2.01
49 50 9.682465 GGATTCTAGGTAAAGAAATGGTAAACT 57.318 33.333 0.00 0.00 38.90 2.66
76 77 5.625568 TTCTAGGTAAGAAATAGGGTGCC 57.374 43.478 0.00 0.00 41.35 5.01
77 78 4.627015 TCTAGGTAAGAAATAGGGTGCCA 58.373 43.478 0.00 0.00 0.00 4.92
78 79 5.224441 TCTAGGTAAGAAATAGGGTGCCAT 58.776 41.667 0.00 0.00 0.00 4.40
79 80 6.387127 TCTAGGTAAGAAATAGGGTGCCATA 58.613 40.000 0.00 0.00 0.00 2.74
80 81 5.306114 AGGTAAGAAATAGGGTGCCATAC 57.694 43.478 0.00 0.00 0.00 2.39
81 82 4.724798 AGGTAAGAAATAGGGTGCCATACA 59.275 41.667 0.00 0.00 0.00 2.29
82 83 5.372661 AGGTAAGAAATAGGGTGCCATACAT 59.627 40.000 0.00 0.00 0.00 2.29
83 84 6.561070 AGGTAAGAAATAGGGTGCCATACATA 59.439 38.462 0.00 0.00 0.00 2.29
84 85 7.073215 AGGTAAGAAATAGGGTGCCATACATAA 59.927 37.037 0.00 0.00 0.00 1.90
85 86 7.888546 GGTAAGAAATAGGGTGCCATACATAAT 59.111 37.037 0.00 0.00 0.00 1.28
86 87 7.765695 AAGAAATAGGGTGCCATACATAATG 57.234 36.000 0.00 0.00 35.15 1.90
87 88 5.711976 AGAAATAGGGTGCCATACATAATGC 59.288 40.000 0.00 0.00 33.92 3.56
88 89 1.896220 AGGGTGCCATACATAATGCG 58.104 50.000 0.00 0.00 33.92 4.73
89 90 0.881118 GGGTGCCATACATAATGCGG 59.119 55.000 0.00 0.00 33.92 5.69
90 91 1.544537 GGGTGCCATACATAATGCGGA 60.545 52.381 0.00 0.00 33.92 5.54
91 92 2.436417 GGTGCCATACATAATGCGGAT 58.564 47.619 0.00 0.00 33.92 4.18
92 93 2.420022 GGTGCCATACATAATGCGGATC 59.580 50.000 0.00 0.00 33.92 3.36
93 94 2.094258 GTGCCATACATAATGCGGATCG 59.906 50.000 0.00 0.00 33.92 3.69
94 95 2.289382 TGCCATACATAATGCGGATCGT 60.289 45.455 0.00 0.00 33.92 3.73
95 96 2.094258 GCCATACATAATGCGGATCGTG 59.906 50.000 0.00 0.00 33.92 4.35
96 97 2.672874 CCATACATAATGCGGATCGTGG 59.327 50.000 0.00 0.00 33.92 4.94
97 98 2.448926 TACATAATGCGGATCGTGGG 57.551 50.000 0.00 0.00 0.00 4.61
98 99 0.756294 ACATAATGCGGATCGTGGGA 59.244 50.000 0.00 0.00 0.00 4.37
99 100 1.140052 ACATAATGCGGATCGTGGGAA 59.860 47.619 0.00 0.00 0.00 3.97
100 101 2.224523 ACATAATGCGGATCGTGGGAAT 60.225 45.455 0.00 0.00 0.00 3.01
101 102 1.877637 TAATGCGGATCGTGGGAATG 58.122 50.000 0.00 0.00 0.00 2.67
102 103 0.819259 AATGCGGATCGTGGGAATGG 60.819 55.000 0.00 0.00 0.00 3.16
103 104 1.695114 ATGCGGATCGTGGGAATGGA 61.695 55.000 0.00 0.00 0.00 3.41
104 105 1.071471 GCGGATCGTGGGAATGGAT 59.929 57.895 0.00 0.00 0.00 3.41
105 106 0.535102 GCGGATCGTGGGAATGGATT 60.535 55.000 0.00 0.00 0.00 3.01
106 107 1.229428 CGGATCGTGGGAATGGATTG 58.771 55.000 0.00 0.00 0.00 2.67
107 108 1.609208 GGATCGTGGGAATGGATTGG 58.391 55.000 0.00 0.00 0.00 3.16
108 109 0.954452 GATCGTGGGAATGGATTGGC 59.046 55.000 0.00 0.00 0.00 4.52
109 110 0.819259 ATCGTGGGAATGGATTGGCG 60.819 55.000 0.00 0.00 0.00 5.69
110 111 2.480610 CGTGGGAATGGATTGGCGG 61.481 63.158 0.00 0.00 0.00 6.13
111 112 1.379843 GTGGGAATGGATTGGCGGT 60.380 57.895 0.00 0.00 0.00 5.68
112 113 0.106918 GTGGGAATGGATTGGCGGTA 60.107 55.000 0.00 0.00 0.00 4.02
113 114 0.182537 TGGGAATGGATTGGCGGTAG 59.817 55.000 0.00 0.00 0.00 3.18
114 115 0.472471 GGGAATGGATTGGCGGTAGA 59.528 55.000 0.00 0.00 0.00 2.59
115 116 1.594331 GGAATGGATTGGCGGTAGAC 58.406 55.000 0.00 0.00 0.00 2.59
131 132 4.113354 GGTAGACGAATCACAGATGAACC 58.887 47.826 0.00 0.00 38.69 3.62
132 133 3.252974 AGACGAATCACAGATGAACCC 57.747 47.619 0.00 0.00 38.69 4.11
133 134 2.567169 AGACGAATCACAGATGAACCCA 59.433 45.455 0.00 0.00 38.69 4.51
134 135 2.932614 GACGAATCACAGATGAACCCAG 59.067 50.000 0.00 0.00 38.69 4.45
135 136 1.667724 CGAATCACAGATGAACCCAGC 59.332 52.381 0.00 0.00 38.69 4.85
136 137 2.019984 GAATCACAGATGAACCCAGCC 58.980 52.381 0.00 0.00 38.69 4.85
137 138 0.994247 ATCACAGATGAACCCAGCCA 59.006 50.000 0.00 0.00 38.69 4.75
138 139 0.325933 TCACAGATGAACCCAGCCAG 59.674 55.000 0.00 0.00 0.00 4.85
139 140 1.001641 ACAGATGAACCCAGCCAGC 60.002 57.895 0.00 0.00 0.00 4.85
140 141 1.302285 CAGATGAACCCAGCCAGCT 59.698 57.895 0.00 0.00 0.00 4.24
141 142 0.747283 CAGATGAACCCAGCCAGCTC 60.747 60.000 0.00 0.00 0.00 4.09
142 143 1.817099 GATGAACCCAGCCAGCTCG 60.817 63.158 0.00 0.00 0.00 5.03
143 144 3.335356 ATGAACCCAGCCAGCTCGG 62.335 63.158 1.35 1.35 38.11 4.63
144 145 3.706373 GAACCCAGCCAGCTCGGA 61.706 66.667 10.47 0.00 36.56 4.55
145 146 3.249189 AACCCAGCCAGCTCGGAA 61.249 61.111 10.47 0.00 36.56 4.30
146 147 3.553095 AACCCAGCCAGCTCGGAAC 62.553 63.158 10.47 0.00 36.56 3.62
147 148 3.710722 CCCAGCCAGCTCGGAACT 61.711 66.667 0.00 0.00 36.56 3.01
148 149 2.125350 CCAGCCAGCTCGGAACTC 60.125 66.667 6.40 0.00 36.56 3.01
149 150 2.654079 CCAGCCAGCTCGGAACTCT 61.654 63.158 6.40 0.00 36.56 3.24
150 151 1.153667 CAGCCAGCTCGGAACTCTC 60.154 63.158 6.40 0.00 36.56 3.20
151 152 2.185608 GCCAGCTCGGAACTCTCC 59.814 66.667 6.40 0.00 36.56 3.71
152 153 2.355193 GCCAGCTCGGAACTCTCCT 61.355 63.158 6.40 0.00 39.93 3.69
153 154 1.515020 CCAGCTCGGAACTCTCCTG 59.485 63.158 0.00 0.00 39.93 3.86
154 155 0.967887 CCAGCTCGGAACTCTCCTGA 60.968 60.000 0.00 0.00 39.93 3.86
155 156 1.110442 CAGCTCGGAACTCTCCTGAT 58.890 55.000 0.00 0.00 39.93 2.90
156 157 2.302260 CAGCTCGGAACTCTCCTGATA 58.698 52.381 0.00 0.00 39.93 2.15
157 158 2.690497 CAGCTCGGAACTCTCCTGATAA 59.310 50.000 0.00 0.00 39.93 1.75
158 159 2.955660 AGCTCGGAACTCTCCTGATAAG 59.044 50.000 0.00 0.00 39.93 1.73
159 160 2.544903 GCTCGGAACTCTCCTGATAAGC 60.545 54.545 0.00 0.00 39.93 3.09
160 161 2.032620 TCGGAACTCTCCTGATAAGCC 58.967 52.381 0.00 0.00 39.93 4.35
161 162 1.269309 CGGAACTCTCCTGATAAGCCG 60.269 57.143 0.00 0.00 39.93 5.52
162 163 1.757699 GGAACTCTCCTGATAAGCCGT 59.242 52.381 0.00 0.00 38.88 5.68
163 164 2.168728 GGAACTCTCCTGATAAGCCGTT 59.831 50.000 0.00 0.00 38.88 4.44
164 165 3.449632 GAACTCTCCTGATAAGCCGTTC 58.550 50.000 0.00 0.00 0.00 3.95
165 166 2.741145 ACTCTCCTGATAAGCCGTTCT 58.259 47.619 0.00 0.00 0.00 3.01
166 167 2.691011 ACTCTCCTGATAAGCCGTTCTC 59.309 50.000 0.00 0.00 0.00 2.87
167 168 2.032620 TCTCCTGATAAGCCGTTCTCC 58.967 52.381 0.00 0.00 0.00 3.71
168 169 2.035632 CTCCTGATAAGCCGTTCTCCT 58.964 52.381 0.00 0.00 0.00 3.69
169 170 2.432510 CTCCTGATAAGCCGTTCTCCTT 59.567 50.000 0.00 0.00 0.00 3.36
170 171 2.168521 TCCTGATAAGCCGTTCTCCTTG 59.831 50.000 0.00 0.00 0.00 3.61
171 172 2.093447 CCTGATAAGCCGTTCTCCTTGT 60.093 50.000 0.00 0.00 0.00 3.16
172 173 2.932614 CTGATAAGCCGTTCTCCTTGTG 59.067 50.000 0.00 0.00 0.00 3.33
173 174 2.565391 TGATAAGCCGTTCTCCTTGTGA 59.435 45.455 0.00 0.00 0.00 3.58
174 175 2.450609 TAAGCCGTTCTCCTTGTGAC 57.549 50.000 0.00 0.00 0.00 3.67
175 176 0.759346 AAGCCGTTCTCCTTGTGACT 59.241 50.000 0.00 0.00 0.00 3.41
176 177 0.034059 AGCCGTTCTCCTTGTGACTG 59.966 55.000 0.00 0.00 0.00 3.51
177 178 0.033504 GCCGTTCTCCTTGTGACTGA 59.966 55.000 0.00 0.00 0.00 3.41
178 179 1.784525 CCGTTCTCCTTGTGACTGAC 58.215 55.000 0.00 0.00 0.00 3.51
179 180 1.341531 CCGTTCTCCTTGTGACTGACT 59.658 52.381 0.00 0.00 0.00 3.41
180 181 2.608261 CCGTTCTCCTTGTGACTGACTC 60.608 54.545 0.00 0.00 0.00 3.36
181 182 2.034685 CGTTCTCCTTGTGACTGACTCA 59.965 50.000 0.00 0.00 0.00 3.41
191 192 3.733337 GTGACTGACTCACCAGAAATGT 58.267 45.455 0.00 0.00 43.35 2.71
192 193 4.883083 GTGACTGACTCACCAGAAATGTA 58.117 43.478 0.00 0.00 43.35 2.29
193 194 4.926238 GTGACTGACTCACCAGAAATGTAG 59.074 45.833 0.00 0.00 43.35 2.74
194 195 4.588951 TGACTGACTCACCAGAAATGTAGT 59.411 41.667 0.00 0.00 37.59 2.73
195 196 4.887748 ACTGACTCACCAGAAATGTAGTG 58.112 43.478 0.00 0.00 37.59 2.74
196 197 4.345257 ACTGACTCACCAGAAATGTAGTGT 59.655 41.667 0.00 0.00 37.59 3.55
197 198 4.883083 TGACTCACCAGAAATGTAGTGTC 58.117 43.478 0.00 0.00 0.00 3.67
198 199 4.588951 TGACTCACCAGAAATGTAGTGTCT 59.411 41.667 0.00 0.00 0.00 3.41
199 200 4.887748 ACTCACCAGAAATGTAGTGTCTG 58.112 43.478 0.00 0.00 38.81 3.51
204 205 5.050091 CACCAGAAATGTAGTGTCTGTCAAC 60.050 44.000 0.00 0.00 37.64 3.18
211 212 4.116961 TGTAGTGTCTGTCAACGGAAAAG 58.883 43.478 0.00 0.00 32.23 2.27
221 222 4.451096 TGTCAACGGAAAAGCTGACTATTC 59.549 41.667 0.00 0.00 37.90 1.75
224 225 6.035112 GTCAACGGAAAAGCTGACTATTCTAG 59.965 42.308 0.00 0.00 35.15 2.43
232 233 3.067461 AGCTGACTATTCTAGTGAAGCGG 59.933 47.826 10.56 0.00 44.10 5.52
249 250 2.046285 GGGGTGCCGAGTCAATTGG 61.046 63.158 5.42 0.00 35.19 3.16
253 254 1.463674 GTGCCGAGTCAATTGGGAAT 58.536 50.000 5.42 0.00 33.90 3.01
257 258 2.159379 GCCGAGTCAATTGGGAATGAAC 60.159 50.000 5.42 0.00 32.21 3.18
260 261 1.468520 AGTCAATTGGGAATGAACGCG 59.531 47.619 3.53 3.53 0.00 6.01
347 348 0.036765 ATGAGGACTTTGCGGCGTTA 60.037 50.000 9.37 0.00 0.00 3.18
353 354 1.296867 CTTTGCGGCGTTATCAGCG 60.297 57.895 9.37 0.00 35.00 5.18
394 396 9.529325 TGATGATGTACTAGTATTAAACTGCAC 57.471 33.333 5.75 0.00 39.39 4.57
448 450 3.081804 AGAATGAAACGGCTCCGAAATT 58.918 40.909 15.95 6.87 42.83 1.82
712 720 4.194678 TGAATAATACTCCCTCGGTCCT 57.805 45.455 0.00 0.00 0.00 3.85
724 732 4.966805 TCCCTCGGTCCTTTAATGTAAGAT 59.033 41.667 0.00 0.00 0.00 2.40
726 734 5.396436 CCCTCGGTCCTTTAATGTAAGATGT 60.396 44.000 0.00 0.00 0.00 3.06
734 742 9.423061 GTCCTTTAATGTAAGATGTTTTTGCAT 57.577 29.630 0.00 0.00 33.20 3.96
738 746 8.984891 TTAATGTAAGATGTTTTTGCATGGAG 57.015 30.769 0.00 0.00 32.37 3.86
741 749 2.181975 AGATGTTTTTGCATGGAGGGG 58.818 47.619 0.00 0.00 0.00 4.79
822 851 2.860735 CTGAACGCTGGTATGAAGTAGC 59.139 50.000 0.00 0.00 0.00 3.58
943 976 1.720694 AAACTTCCACAACGCCCGTG 61.721 55.000 0.00 0.00 0.00 4.94
1081 1116 8.942338 ATTAGTTCACAGTAATCGCAGATTAA 57.058 30.769 10.99 0.00 45.12 1.40
1089 1124 2.622064 ATCGCAGATTAACACTCCCC 57.378 50.000 0.00 0.00 45.12 4.81
1090 1125 0.539986 TCGCAGATTAACACTCCCCC 59.460 55.000 0.00 0.00 0.00 5.40
1091 1126 0.541863 CGCAGATTAACACTCCCCCT 59.458 55.000 0.00 0.00 0.00 4.79
1092 1127 1.473434 CGCAGATTAACACTCCCCCTC 60.473 57.143 0.00 0.00 0.00 4.30
1093 1128 1.134068 GCAGATTAACACTCCCCCTCC 60.134 57.143 0.00 0.00 0.00 4.30
1094 1129 1.139058 CAGATTAACACTCCCCCTCCG 59.861 57.143 0.00 0.00 0.00 4.63
1095 1130 0.468648 GATTAACACTCCCCCTCCGG 59.531 60.000 0.00 0.00 0.00 5.14
1121 1156 1.075601 GCCATCCTATCCCATTCCCA 58.924 55.000 0.00 0.00 0.00 4.37
1130 1165 1.153168 CCCATTCCCAGCTACACCG 60.153 63.158 0.00 0.00 0.00 4.94
2064 2120 1.174078 TCGACGGCTGTCAAGGTACA 61.174 55.000 24.91 0.00 45.80 2.90
2066 2122 1.006571 ACGGCTGTCAAGGTACACG 60.007 57.895 0.00 0.00 0.00 4.49
2068 2124 1.007336 CGGCTGTCAAGGTACACGTC 61.007 60.000 0.00 0.00 0.00 4.34
2071 2127 2.059541 GCTGTCAAGGTACACGTCTTC 58.940 52.381 0.00 0.00 0.00 2.87
2072 2128 2.673833 CTGTCAAGGTACACGTCTTCC 58.326 52.381 0.00 0.00 0.00 3.46
2076 2132 2.413837 CAAGGTACACGTCTTCCCTTG 58.586 52.381 14.72 14.72 44.29 3.61
2100 2184 0.249447 GGTTGCTTGTTTCCACTGCC 60.249 55.000 0.00 0.00 0.00 4.85
2106 2190 2.665185 GTTTCCACTGCCGCGAGT 60.665 61.111 8.23 0.00 0.00 4.18
2107 2191 2.110213 TTTCCACTGCCGCGAGTT 59.890 55.556 8.23 0.00 0.00 3.01
2108 2192 1.959226 TTTCCACTGCCGCGAGTTC 60.959 57.895 8.23 0.00 0.00 3.01
2109 2193 2.652382 TTTCCACTGCCGCGAGTTCA 62.652 55.000 8.23 0.00 0.00 3.18
2110 2194 3.414700 CCACTGCCGCGAGTTCAC 61.415 66.667 8.23 0.00 0.00 3.18
2144 2228 3.369400 CATGCCCGGCCGTTTTGA 61.369 61.111 26.12 2.95 0.00 2.69
2145 2229 2.362375 ATGCCCGGCCGTTTTGAT 60.362 55.556 26.12 5.46 0.00 2.57
2157 2241 1.128692 CGTTTTGATCGCCTTGTCCTC 59.871 52.381 0.00 0.00 0.00 3.71
2169 2253 3.805108 GCCTTGTCCTCGCAGATATCAAT 60.805 47.826 5.32 0.00 33.89 2.57
2253 2343 2.670934 AGCTGCGTTTGCCCTGAG 60.671 61.111 0.00 0.00 41.78 3.35
2356 2451 3.881220 TCGATGTTATTTCTGGGGTTCC 58.119 45.455 0.00 0.00 0.00 3.62
2402 2503 3.366273 GGTGTAACGTCCATTCGTACTGA 60.366 47.826 0.00 0.00 43.38 3.41
2705 2870 1.598701 GGTGGCCATCAAGAAGTGCC 61.599 60.000 12.38 0.00 42.49 5.01
3024 3208 0.454600 TCCAACATACTCCTCGACGC 59.545 55.000 0.00 0.00 0.00 5.19
3271 3464 1.153939 CCTCTCGTCGCAGTTCCTG 60.154 63.158 0.00 0.00 34.12 3.86
3610 3803 3.391049 GGCGTACATAGGAATTCAGTCC 58.609 50.000 7.93 0.00 38.03 3.85
3696 3889 2.749076 TCTCCCGATTGATGCAAACAAG 59.251 45.455 13.46 3.62 30.05 3.16
3699 3892 3.191162 TCCCGATTGATGCAAACAAGAAG 59.809 43.478 13.46 8.21 30.05 2.85
3709 3902 4.757594 TGCAAACAAGAAGTGAAGCATTT 58.242 34.783 0.00 0.00 30.78 2.32
3750 3944 8.983724 CCCATTTGTACGTTTTTGACATATTTT 58.016 29.630 0.00 0.00 0.00 1.82
3807 4002 1.356494 TGGTGATGTGGGTTGGGTCA 61.356 55.000 0.00 0.00 0.00 4.02
3814 4009 1.151899 TGGGTTGGGTCAGGCTACT 60.152 57.895 0.00 0.00 0.00 2.57
3837 4032 1.843851 AGGCCATTTCTAACCGATCCA 59.156 47.619 5.01 0.00 0.00 3.41
3862 4057 9.151471 CATAATAAATAGTGAAGTATCCGGTGG 57.849 37.037 0.00 0.00 0.00 4.61
4203 6945 5.796424 AATGCCACAGAATTTTTGAGAGT 57.204 34.783 0.00 0.00 0.00 3.24
4215 6957 8.127327 AGAATTTTTGAGAGTTCATATGATGCG 58.873 33.333 6.17 0.00 32.27 4.73
4281 7023 6.849588 AATTTTGAGCACAACTTCCATTTC 57.150 33.333 0.00 0.00 35.63 2.17
4383 7127 1.686587 GTCCTTCCAACCAAACCCTTG 59.313 52.381 0.00 0.00 0.00 3.61
4393 7137 2.243736 ACCAAACCCTTGAGTCCAGAAA 59.756 45.455 0.00 0.00 34.14 2.52
4522 7266 3.244911 ACCAACTCCACCACCATCTTTAG 60.245 47.826 0.00 0.00 0.00 1.85
4555 7300 0.682209 CTCCACCTGCCAATTCCCAG 60.682 60.000 0.00 0.00 0.00 4.45
4562 7307 2.091665 CCTGCCAATTCCCAGGTCTAAT 60.092 50.000 11.22 0.00 42.87 1.73
4563 7308 3.628257 CCTGCCAATTCCCAGGTCTAATT 60.628 47.826 11.22 0.00 42.87 1.40
4564 7309 4.026052 CTGCCAATTCCCAGGTCTAATTT 58.974 43.478 0.00 0.00 0.00 1.82
4565 7310 4.424842 TGCCAATTCCCAGGTCTAATTTT 58.575 39.130 0.00 0.00 0.00 1.82
4566 7311 4.843516 TGCCAATTCCCAGGTCTAATTTTT 59.156 37.500 0.00 0.00 0.00 1.94
4591 7336 2.290071 ACCAAGGTCACCCTAACATTCG 60.290 50.000 0.00 0.00 41.56 3.34
4613 7358 3.515630 GTCGAACATCTTGAGCTCATGA 58.484 45.455 28.44 28.44 35.04 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.150827 TGAATCTTGTGCGCACTGAG 58.849 50.000 37.59 31.91 0.00 3.35
2 3 1.592064 TTGAATCTTGTGCGCACTGA 58.408 45.000 37.59 32.48 0.00 3.41
4 5 1.267806 CCTTTGAATCTTGTGCGCACT 59.732 47.619 37.59 20.25 0.00 4.40
5 6 1.266718 TCCTTTGAATCTTGTGCGCAC 59.733 47.619 33.11 33.11 0.00 5.34
6 7 1.603456 TCCTTTGAATCTTGTGCGCA 58.397 45.000 5.66 5.66 0.00 6.09
7 8 2.927553 ATCCTTTGAATCTTGTGCGC 57.072 45.000 0.00 0.00 0.00 6.09
8 9 4.691860 AGAATCCTTTGAATCTTGTGCG 57.308 40.909 0.00 0.00 25.46 5.34
9 10 5.649831 ACCTAGAATCCTTTGAATCTTGTGC 59.350 40.000 0.00 0.00 32.90 4.57
10 11 8.792830 TTACCTAGAATCCTTTGAATCTTGTG 57.207 34.615 0.00 0.00 32.90 3.33
11 12 9.454859 CTTTACCTAGAATCCTTTGAATCTTGT 57.545 33.333 0.00 0.00 32.90 3.16
12 13 9.672673 TCTTTACCTAGAATCCTTTGAATCTTG 57.327 33.333 0.00 0.00 32.90 3.02
17 18 9.243105 CCATTTCTTTACCTAGAATCCTTTGAA 57.757 33.333 0.00 0.00 34.33 2.69
18 19 8.390921 ACCATTTCTTTACCTAGAATCCTTTGA 58.609 33.333 0.00 0.00 34.33 2.69
19 20 8.581253 ACCATTTCTTTACCTAGAATCCTTTG 57.419 34.615 0.00 0.00 34.33 2.77
22 23 9.682465 GTTTACCATTTCTTTACCTAGAATCCT 57.318 33.333 0.00 0.00 34.33 3.24
23 24 9.682465 AGTTTACCATTTCTTTACCTAGAATCC 57.318 33.333 0.00 0.00 34.33 3.01
54 55 5.034200 TGGCACCCTATTTCTTACCTAGAA 58.966 41.667 0.00 0.00 41.11 2.10
55 56 4.627015 TGGCACCCTATTTCTTACCTAGA 58.373 43.478 0.00 0.00 0.00 2.43
56 57 5.568620 ATGGCACCCTATTTCTTACCTAG 57.431 43.478 0.00 0.00 0.00 3.02
57 58 5.906495 TGTATGGCACCCTATTTCTTACCTA 59.094 40.000 0.00 0.00 0.00 3.08
58 59 4.724798 TGTATGGCACCCTATTTCTTACCT 59.275 41.667 0.00 0.00 0.00 3.08
59 60 5.043737 TGTATGGCACCCTATTTCTTACC 57.956 43.478 0.00 0.00 0.00 2.85
60 61 8.730680 CATTATGTATGGCACCCTATTTCTTAC 58.269 37.037 0.00 0.00 0.00 2.34
61 62 7.393234 GCATTATGTATGGCACCCTATTTCTTA 59.607 37.037 0.00 0.00 34.66 2.10
62 63 6.209391 GCATTATGTATGGCACCCTATTTCTT 59.791 38.462 0.00 0.00 34.66 2.52
63 64 5.711976 GCATTATGTATGGCACCCTATTTCT 59.288 40.000 0.00 0.00 34.66 2.52
64 65 5.391950 CGCATTATGTATGGCACCCTATTTC 60.392 44.000 0.00 0.00 34.66 2.17
65 66 4.458989 CGCATTATGTATGGCACCCTATTT 59.541 41.667 0.00 0.00 34.66 1.40
66 67 4.009675 CGCATTATGTATGGCACCCTATT 58.990 43.478 0.00 0.00 34.66 1.73
67 68 3.609853 CGCATTATGTATGGCACCCTAT 58.390 45.455 0.00 0.00 34.66 2.57
68 69 2.290008 CCGCATTATGTATGGCACCCTA 60.290 50.000 0.00 0.00 34.66 3.53
69 70 1.545428 CCGCATTATGTATGGCACCCT 60.545 52.381 0.00 0.00 34.66 4.34
70 71 0.881118 CCGCATTATGTATGGCACCC 59.119 55.000 0.00 0.00 34.66 4.61
71 72 1.890876 TCCGCATTATGTATGGCACC 58.109 50.000 0.00 0.00 34.66 5.01
72 73 2.094258 CGATCCGCATTATGTATGGCAC 59.906 50.000 0.00 0.00 34.66 5.01
73 74 2.289382 ACGATCCGCATTATGTATGGCA 60.289 45.455 0.00 0.00 34.66 4.92
74 75 2.094258 CACGATCCGCATTATGTATGGC 59.906 50.000 0.00 0.00 34.66 4.40
75 76 2.672874 CCACGATCCGCATTATGTATGG 59.327 50.000 0.00 0.00 34.66 2.74
76 77 2.672874 CCCACGATCCGCATTATGTATG 59.327 50.000 0.00 0.00 37.31 2.39
77 78 2.565391 TCCCACGATCCGCATTATGTAT 59.435 45.455 0.00 0.00 0.00 2.29
78 79 1.964933 TCCCACGATCCGCATTATGTA 59.035 47.619 0.00 0.00 0.00 2.29
79 80 0.756294 TCCCACGATCCGCATTATGT 59.244 50.000 0.00 0.00 0.00 2.29
80 81 1.877637 TTCCCACGATCCGCATTATG 58.122 50.000 0.00 0.00 0.00 1.90
81 82 2.426522 CATTCCCACGATCCGCATTAT 58.573 47.619 0.00 0.00 0.00 1.28
82 83 1.542328 CCATTCCCACGATCCGCATTA 60.542 52.381 0.00 0.00 0.00 1.90
83 84 0.819259 CCATTCCCACGATCCGCATT 60.819 55.000 0.00 0.00 0.00 3.56
84 85 1.227943 CCATTCCCACGATCCGCAT 60.228 57.895 0.00 0.00 0.00 4.73
85 86 1.695114 ATCCATTCCCACGATCCGCA 61.695 55.000 0.00 0.00 0.00 5.69
86 87 0.535102 AATCCATTCCCACGATCCGC 60.535 55.000 0.00 0.00 0.00 5.54
87 88 1.229428 CAATCCATTCCCACGATCCG 58.771 55.000 0.00 0.00 0.00 4.18
88 89 1.609208 CCAATCCATTCCCACGATCC 58.391 55.000 0.00 0.00 0.00 3.36
89 90 0.954452 GCCAATCCATTCCCACGATC 59.046 55.000 0.00 0.00 0.00 3.69
90 91 0.819259 CGCCAATCCATTCCCACGAT 60.819 55.000 0.00 0.00 0.00 3.73
91 92 1.451207 CGCCAATCCATTCCCACGA 60.451 57.895 0.00 0.00 0.00 4.35
92 93 2.480610 CCGCCAATCCATTCCCACG 61.481 63.158 0.00 0.00 0.00 4.94
93 94 0.106918 TACCGCCAATCCATTCCCAC 60.107 55.000 0.00 0.00 0.00 4.61
94 95 0.182537 CTACCGCCAATCCATTCCCA 59.817 55.000 0.00 0.00 0.00 4.37
95 96 0.472471 TCTACCGCCAATCCATTCCC 59.528 55.000 0.00 0.00 0.00 3.97
96 97 1.594331 GTCTACCGCCAATCCATTCC 58.406 55.000 0.00 0.00 0.00 3.01
97 98 1.202486 TCGTCTACCGCCAATCCATTC 60.202 52.381 0.00 0.00 36.19 2.67
98 99 0.828022 TCGTCTACCGCCAATCCATT 59.172 50.000 0.00 0.00 36.19 3.16
99 100 0.828022 TTCGTCTACCGCCAATCCAT 59.172 50.000 0.00 0.00 36.19 3.41
100 101 0.828022 ATTCGTCTACCGCCAATCCA 59.172 50.000 0.00 0.00 36.19 3.41
101 102 1.202486 TGATTCGTCTACCGCCAATCC 60.202 52.381 0.00 0.00 31.96 3.01
102 103 1.859080 GTGATTCGTCTACCGCCAATC 59.141 52.381 0.00 0.00 36.19 2.67
103 104 1.206132 TGTGATTCGTCTACCGCCAAT 59.794 47.619 0.00 0.00 36.19 3.16
104 105 0.604073 TGTGATTCGTCTACCGCCAA 59.396 50.000 0.00 0.00 36.19 4.52
105 106 0.172578 CTGTGATTCGTCTACCGCCA 59.827 55.000 0.00 0.00 36.19 5.69
106 107 0.454600 TCTGTGATTCGTCTACCGCC 59.545 55.000 0.00 0.00 36.19 6.13
107 108 2.120232 CATCTGTGATTCGTCTACCGC 58.880 52.381 0.00 0.00 36.19 5.68
108 109 3.692791 TCATCTGTGATTCGTCTACCG 57.307 47.619 0.00 0.00 38.13 4.02
109 110 4.113354 GGTTCATCTGTGATTCGTCTACC 58.887 47.826 0.00 0.00 33.56 3.18
110 111 4.113354 GGGTTCATCTGTGATTCGTCTAC 58.887 47.826 0.00 0.00 33.56 2.59
111 112 3.767131 TGGGTTCATCTGTGATTCGTCTA 59.233 43.478 0.00 0.00 33.56 2.59
112 113 2.567169 TGGGTTCATCTGTGATTCGTCT 59.433 45.455 0.00 0.00 33.56 4.18
113 114 2.932614 CTGGGTTCATCTGTGATTCGTC 59.067 50.000 0.00 0.00 33.56 4.20
114 115 2.936993 GCTGGGTTCATCTGTGATTCGT 60.937 50.000 0.00 0.00 33.56 3.85
115 116 1.667724 GCTGGGTTCATCTGTGATTCG 59.332 52.381 0.00 0.00 33.56 3.34
116 117 2.019984 GGCTGGGTTCATCTGTGATTC 58.980 52.381 0.00 0.00 33.56 2.52
117 118 1.355381 TGGCTGGGTTCATCTGTGATT 59.645 47.619 0.00 0.00 33.56 2.57
118 119 0.994247 TGGCTGGGTTCATCTGTGAT 59.006 50.000 0.00 0.00 33.56 3.06
119 120 0.325933 CTGGCTGGGTTCATCTGTGA 59.674 55.000 0.00 0.00 0.00 3.58
120 121 1.310933 GCTGGCTGGGTTCATCTGTG 61.311 60.000 0.00 0.00 0.00 3.66
121 122 1.001641 GCTGGCTGGGTTCATCTGT 60.002 57.895 0.00 0.00 0.00 3.41
122 123 0.747283 GAGCTGGCTGGGTTCATCTG 60.747 60.000 0.00 0.00 0.00 2.90
123 124 1.606531 GAGCTGGCTGGGTTCATCT 59.393 57.895 0.00 0.00 0.00 2.90
124 125 1.817099 CGAGCTGGCTGGGTTCATC 60.817 63.158 0.00 0.00 0.00 2.92
125 126 2.270205 CGAGCTGGCTGGGTTCAT 59.730 61.111 0.00 0.00 0.00 2.57
126 127 4.020617 CCGAGCTGGCTGGGTTCA 62.021 66.667 14.16 0.00 37.20 3.18
127 128 3.254024 TTCCGAGCTGGCTGGGTTC 62.254 63.158 19.97 0.00 41.77 3.62
128 129 3.249189 TTCCGAGCTGGCTGGGTT 61.249 61.111 19.97 0.00 41.77 4.11
129 130 4.021925 GTTCCGAGCTGGCTGGGT 62.022 66.667 19.97 0.00 41.77 4.51
130 131 3.672295 GAGTTCCGAGCTGGCTGGG 62.672 68.421 15.86 15.86 42.33 4.45
131 132 2.125350 GAGTTCCGAGCTGGCTGG 60.125 66.667 0.00 0.00 37.80 4.85
132 133 1.153667 GAGAGTTCCGAGCTGGCTG 60.154 63.158 0.00 0.00 37.80 4.85
133 134 2.355193 GGAGAGTTCCGAGCTGGCT 61.355 63.158 0.00 0.00 37.80 4.75
134 135 2.185608 GGAGAGTTCCGAGCTGGC 59.814 66.667 0.00 0.00 37.80 4.85
142 143 1.757699 ACGGCTTATCAGGAGAGTTCC 59.242 52.381 0.00 0.00 44.39 3.62
143 144 3.131400 AGAACGGCTTATCAGGAGAGTTC 59.869 47.826 0.00 0.00 35.48 3.01
144 145 3.100671 AGAACGGCTTATCAGGAGAGTT 58.899 45.455 0.00 0.00 0.00 3.01
145 146 2.691011 GAGAACGGCTTATCAGGAGAGT 59.309 50.000 0.00 0.00 0.00 3.24
146 147 2.035321 GGAGAACGGCTTATCAGGAGAG 59.965 54.545 0.00 0.00 0.00 3.20
147 148 2.032620 GGAGAACGGCTTATCAGGAGA 58.967 52.381 0.00 0.00 0.00 3.71
148 149 2.035632 AGGAGAACGGCTTATCAGGAG 58.964 52.381 0.00 0.00 0.00 3.69
149 150 2.160721 AGGAGAACGGCTTATCAGGA 57.839 50.000 0.00 0.00 0.00 3.86
150 151 2.093447 ACAAGGAGAACGGCTTATCAGG 60.093 50.000 0.00 0.00 0.00 3.86
151 152 2.932614 CACAAGGAGAACGGCTTATCAG 59.067 50.000 0.00 0.00 0.00 2.90
152 153 2.565391 TCACAAGGAGAACGGCTTATCA 59.435 45.455 0.00 0.00 0.00 2.15
153 154 2.930682 GTCACAAGGAGAACGGCTTATC 59.069 50.000 0.00 0.00 0.00 1.75
154 155 2.567615 AGTCACAAGGAGAACGGCTTAT 59.432 45.455 0.00 0.00 0.00 1.73
155 156 1.968493 AGTCACAAGGAGAACGGCTTA 59.032 47.619 0.00 0.00 0.00 3.09
156 157 0.759346 AGTCACAAGGAGAACGGCTT 59.241 50.000 0.00 0.00 0.00 4.35
157 158 0.034059 CAGTCACAAGGAGAACGGCT 59.966 55.000 0.00 0.00 0.00 5.52
158 159 0.033504 TCAGTCACAAGGAGAACGGC 59.966 55.000 0.00 0.00 0.00 5.68
159 160 1.341531 AGTCAGTCACAAGGAGAACGG 59.658 52.381 0.00 0.00 0.00 4.44
160 161 2.034685 TGAGTCAGTCACAAGGAGAACG 59.965 50.000 0.00 0.00 0.00 3.95
161 162 3.735237 TGAGTCAGTCACAAGGAGAAC 57.265 47.619 0.00 0.00 0.00 3.01
171 172 4.588951 ACTACATTTCTGGTGAGTCAGTCA 59.411 41.667 0.00 0.00 36.25 3.41
172 173 4.926238 CACTACATTTCTGGTGAGTCAGTC 59.074 45.833 0.00 0.00 36.25 3.51
173 174 4.345257 ACACTACATTTCTGGTGAGTCAGT 59.655 41.667 0.00 0.00 36.25 3.41
174 175 4.887748 ACACTACATTTCTGGTGAGTCAG 58.112 43.478 0.00 0.00 36.17 3.51
175 176 4.588951 AGACACTACATTTCTGGTGAGTCA 59.411 41.667 0.00 0.00 34.28 3.41
176 177 4.926238 CAGACACTACATTTCTGGTGAGTC 59.074 45.833 0.00 0.00 34.31 3.36
177 178 4.345257 ACAGACACTACATTTCTGGTGAGT 59.655 41.667 3.09 0.00 41.00 3.41
178 179 4.887748 ACAGACACTACATTTCTGGTGAG 58.112 43.478 3.09 0.00 41.00 3.51
179 180 4.343814 TGACAGACACTACATTTCTGGTGA 59.656 41.667 3.09 0.00 41.00 4.02
180 181 4.631131 TGACAGACACTACATTTCTGGTG 58.369 43.478 3.09 0.00 41.00 4.17
181 182 4.955811 TGACAGACACTACATTTCTGGT 57.044 40.909 3.09 0.00 41.00 4.00
182 183 4.150627 CGTTGACAGACACTACATTTCTGG 59.849 45.833 3.09 0.00 41.00 3.86
183 184 4.150627 CCGTTGACAGACACTACATTTCTG 59.849 45.833 0.00 0.00 42.17 3.02
184 185 4.038763 TCCGTTGACAGACACTACATTTCT 59.961 41.667 0.00 0.00 0.00 2.52
185 186 4.304110 TCCGTTGACAGACACTACATTTC 58.696 43.478 0.00 0.00 0.00 2.17
186 187 4.330944 TCCGTTGACAGACACTACATTT 57.669 40.909 0.00 0.00 0.00 2.32
187 188 4.330944 TTCCGTTGACAGACACTACATT 57.669 40.909 0.00 0.00 0.00 2.71
188 189 4.330944 TTTCCGTTGACAGACACTACAT 57.669 40.909 0.00 0.00 0.00 2.29
189 190 3.804786 TTTCCGTTGACAGACACTACA 57.195 42.857 0.00 0.00 0.00 2.74
190 191 3.059800 GCTTTTCCGTTGACAGACACTAC 60.060 47.826 0.00 0.00 0.00 2.73
191 192 3.128349 GCTTTTCCGTTGACAGACACTA 58.872 45.455 0.00 0.00 0.00 2.74
192 193 1.940613 GCTTTTCCGTTGACAGACACT 59.059 47.619 0.00 0.00 0.00 3.55
193 194 1.940613 AGCTTTTCCGTTGACAGACAC 59.059 47.619 0.00 0.00 0.00 3.67
194 195 1.939934 CAGCTTTTCCGTTGACAGACA 59.060 47.619 0.00 0.00 0.00 3.41
195 196 2.032808 GTCAGCTTTTCCGTTGACAGAC 60.033 50.000 3.45 0.00 42.46 3.51
196 197 2.158957 AGTCAGCTTTTCCGTTGACAGA 60.159 45.455 9.75 0.00 44.45 3.41
197 198 2.213499 AGTCAGCTTTTCCGTTGACAG 58.787 47.619 9.75 0.00 44.45 3.51
198 199 2.325583 AGTCAGCTTTTCCGTTGACA 57.674 45.000 9.75 0.00 44.45 3.58
199 200 4.691216 AGAATAGTCAGCTTTTCCGTTGAC 59.309 41.667 0.00 0.00 43.00 3.18
221 222 2.125106 GGCACCCCGCTTCACTAG 60.125 66.667 0.00 0.00 41.91 2.57
232 233 2.046285 CCCAATTGACTCGGCACCC 61.046 63.158 7.12 0.00 0.00 4.61
249 250 2.030457 CCAGTCATTACGCGTTCATTCC 59.970 50.000 20.78 1.28 0.00 3.01
253 254 2.665649 ATCCAGTCATTACGCGTTCA 57.334 45.000 20.78 4.87 0.00 3.18
257 258 2.535984 GTCTGAATCCAGTCATTACGCG 59.464 50.000 3.53 3.53 41.16 6.01
353 354 4.639310 ACATCATCAAGAATGTCAGCCTTC 59.361 41.667 0.00 0.00 36.68 3.46
394 396 3.183754 TCGGTCACGCAATATTACAGTG 58.816 45.455 9.52 9.52 40.69 3.66
430 432 2.420022 CAGAATTTCGGAGCCGTTTCAT 59.580 45.455 8.96 0.00 40.74 2.57
694 702 6.557633 ACATTAAAGGACCGAGGGAGTATTAT 59.442 38.462 0.00 0.00 0.00 1.28
697 705 4.296056 ACATTAAAGGACCGAGGGAGTAT 58.704 43.478 0.00 0.00 0.00 2.12
705 713 7.989416 AAAACATCTTACATTAAAGGACCGA 57.011 32.000 0.00 0.00 0.00 4.69
712 720 9.421806 CTCCATGCAAAAACATCTTACATTAAA 57.578 29.630 0.00 0.00 0.00 1.52
724 732 0.105246 ACCCCCTCCATGCAAAAACA 60.105 50.000 0.00 0.00 0.00 2.83
726 734 1.888826 CGTACCCCCTCCATGCAAAAA 60.889 52.381 0.00 0.00 0.00 1.94
734 742 0.548197 ATGAAACCGTACCCCCTCCA 60.548 55.000 0.00 0.00 0.00 3.86
738 746 1.003928 ACAAGATGAAACCGTACCCCC 59.996 52.381 0.00 0.00 0.00 5.40
741 749 3.921677 TCTGACAAGATGAAACCGTACC 58.078 45.455 0.00 0.00 0.00 3.34
822 851 2.286294 CCGAAAAGGATCGATTGCTCTG 59.714 50.000 0.00 0.00 45.48 3.35
943 976 4.143179 GCCTGACTTAATTACACGACACAC 60.143 45.833 0.00 0.00 0.00 3.82
976 1009 3.952508 ATGTCCCACCTGCACGCA 61.953 61.111 0.00 0.00 0.00 5.24
977 1010 3.434319 CATGTCCCACCTGCACGC 61.434 66.667 0.00 0.00 0.00 5.34
978 1011 2.520465 TAGCATGTCCCACCTGCACG 62.520 60.000 6.67 0.00 41.32 5.34
1073 1108 1.134068 GGAGGGGGAGTGTTAATCTGC 60.134 57.143 0.00 0.00 0.00 4.26
1096 1131 2.665603 GGATAGGATGGCCGGAGC 59.334 66.667 5.05 0.00 39.96 4.70
1100 1135 0.035056 GGAATGGGATAGGATGGCCG 60.035 60.000 0.00 0.00 39.96 6.13
1150 1185 1.339610 CGCGAGGATCATCTTCTTCCT 59.660 52.381 0.00 0.00 42.58 3.36
1998 2054 0.737715 CGGAGCAGTTGCAGAGGTAC 60.738 60.000 6.90 0.00 45.16 3.34
2064 2120 0.544697 ACCAACACAAGGGAAGACGT 59.455 50.000 0.00 0.00 0.00 4.34
2066 2122 1.067060 GCAACCAACACAAGGGAAGAC 59.933 52.381 0.00 0.00 0.00 3.01
2068 2124 1.402787 AGCAACCAACACAAGGGAAG 58.597 50.000 0.00 0.00 0.00 3.46
2071 2127 0.823460 ACAAGCAACCAACACAAGGG 59.177 50.000 0.00 0.00 0.00 3.95
2072 2128 2.671130 AACAAGCAACCAACACAAGG 57.329 45.000 0.00 0.00 0.00 3.61
2076 2132 2.094234 AGTGGAAACAAGCAACCAACAC 60.094 45.455 0.00 0.00 46.06 3.32
2100 2184 0.439985 CACCATGAAGTGAACTCGCG 59.560 55.000 0.00 0.00 40.34 5.87
2108 2192 4.359706 CATGCATGAATCACCATGAAGTG 58.640 43.478 22.59 0.00 44.98 3.16
2109 2193 3.181479 GCATGCATGAATCACCATGAAGT 60.181 43.478 30.64 0.00 44.98 3.01
2110 2194 3.381045 GCATGCATGAATCACCATGAAG 58.619 45.455 30.64 0.00 44.98 3.02
2144 2228 1.680522 ATCTGCGAGGACAAGGCGAT 61.681 55.000 0.00 0.00 0.00 4.58
2145 2229 1.035385 TATCTGCGAGGACAAGGCGA 61.035 55.000 0.00 0.00 0.00 5.54
2157 2241 2.486918 TGGCACTCATTGATATCTGCG 58.513 47.619 3.98 0.00 0.00 5.18
2169 2253 1.300620 CCGTTCGTCTTGGCACTCA 60.301 57.895 0.00 0.00 0.00 3.41
2253 2343 1.089920 ATGCGTTGCCTGATGTCTTC 58.910 50.000 0.00 0.00 0.00 2.87
2370 2465 7.223193 CGAATGGACGTTACACCAATTATCTTA 59.777 37.037 0.00 0.00 39.69 2.10
2373 2468 5.292589 ACGAATGGACGTTACACCAATTATC 59.707 40.000 0.00 0.00 44.14 1.75
2374 2469 5.180271 ACGAATGGACGTTACACCAATTAT 58.820 37.500 0.00 0.00 44.14 1.28
2375 2470 4.567971 ACGAATGGACGTTACACCAATTA 58.432 39.130 0.00 0.00 44.14 1.40
2377 2472 3.048337 ACGAATGGACGTTACACCAAT 57.952 42.857 0.00 0.00 44.14 3.16
2379 2474 2.557924 AGTACGAATGGACGTTACACCA 59.442 45.455 0.00 0.00 44.14 4.17
2380 2475 2.919229 CAGTACGAATGGACGTTACACC 59.081 50.000 0.00 0.00 44.14 4.16
2381 2476 3.825308 TCAGTACGAATGGACGTTACAC 58.175 45.455 0.00 0.00 44.14 2.90
2383 2478 4.259690 GCAATCAGTACGAATGGACGTTAC 60.260 45.833 0.00 0.00 44.14 2.50
2402 2503 2.437359 GCTGACTCCTGCGGCAAT 60.437 61.111 3.44 0.00 37.58 3.56
3024 3208 2.125673 CCTTGGCCGTGTAGTCCG 60.126 66.667 0.00 0.00 0.00 4.79
3271 3464 2.683933 TTCTCCCCGAGGACCAGC 60.684 66.667 0.00 0.00 37.19 4.85
3472 3665 0.249657 CCACTAGCTCCGCAGAATCC 60.250 60.000 0.00 0.00 0.00 3.01
3709 3902 1.455822 ATGGGGAGTGGAGGTGAAAA 58.544 50.000 0.00 0.00 0.00 2.29
3718 3912 2.194201 AACGTACAAATGGGGAGTGG 57.806 50.000 0.00 0.00 0.00 4.00
3719 3913 4.036971 TCAAAAACGTACAAATGGGGAGTG 59.963 41.667 0.00 0.00 0.00 3.51
3781 3976 1.303948 CCCACATCACCATGCCAGA 59.696 57.895 0.00 0.00 32.57 3.86
3814 4009 4.080243 TGGATCGGTTAGAAATGGCCTTAA 60.080 41.667 3.32 0.00 0.00 1.85
3837 4032 9.096823 TCCACCGGATACTTCACTATTTATTAT 57.903 33.333 9.46 0.00 0.00 1.28
4177 6918 8.370182 ACTCTCAAAAATTCTGTGGCATTTTAT 58.630 29.630 0.00 0.00 32.54 1.40
4203 6945 9.710900 AAAAGTGATCTATACGCATCATATGAA 57.289 29.630 9.99 0.00 31.71 2.57
4215 6957 9.076596 GGATTTTTGCACAAAAGTGATCTATAC 57.923 33.333 8.38 0.00 40.83 1.47
4281 7023 4.219070 TGCTCAAATTGGACCAGAATTGAG 59.781 41.667 26.21 26.21 0.00 3.02
4344 7087 7.363007 GGAAGGACTATGAGGTGGAAATTTTTC 60.363 40.741 0.00 0.00 36.46 2.29
4383 7127 5.893897 AATTGAGCTGATTTTCTGGACTC 57.106 39.130 0.00 0.00 0.00 3.36
4393 7137 4.464951 TCCAAGATGCAAATTGAGCTGATT 59.535 37.500 14.08 0.00 0.00 2.57
4522 7266 1.202818 GGTGGAGGTATCCTTGGATGC 60.203 57.143 12.08 10.43 46.80 3.91
4591 7336 2.370281 TGAGCTCAAGATGTTCGACC 57.630 50.000 15.67 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.