Multiple sequence alignment - TraesCS2D01G591100

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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 TraesCS2D01G591100 chr2D 100.000 3116 0 0 1 3116 646607562 646610677 0.000000e+00 5755.0
1 TraesCS2D01G591100 chr2D 92.279 1632 48 24 252 1812 647232161 647233785 0.000000e+00 2244.0
2 TraesCS2D01G591100 chr2D 94.328 811 43 2 1470 2278 646252331 646253140 0.000000e+00 1240.0
3 TraesCS2D01G591100 chr2D 89.835 846 65 11 1441 2284 646445149 646444323 0.000000e+00 1066.0
4 TraesCS2D01G591100 chr2D 95.053 283 14 0 1037 1319 646252051 646252333 2.200000e-121 446.0
5 TraesCS2D01G591100 chr2D 89.231 325 23 4 970 1291 646445472 646445157 2.250000e-106 396.0
6 TraesCS2D01G591100 chr2B 94.042 1947 75 20 371 2277 788686736 788684791 0.000000e+00 2915.0
7 TraesCS2D01G591100 chr2B 93.970 597 23 5 2399 2992 788684317 788683731 0.000000e+00 891.0
8 TraesCS2D01G591100 chr2B 88.571 630 52 10 1634 2245 788988977 788989604 0.000000e+00 747.0
9 TraesCS2D01G591100 chr2B 97.166 247 7 0 1 247 77779350 77779596 4.810000e-113 418.0
10 TraesCS2D01G591100 chr2B 95.918 98 4 0 3019 3116 788683731 788683634 3.220000e-35 159.0
11 TraesCS2D01G591100 chr7A 91.929 2094 94 27 254 2278 227081966 227084053 0.000000e+00 2861.0
12 TraesCS2D01G591100 chr7A 96.735 245 8 0 1 245 632652405 632652161 2.890000e-110 409.0
13 TraesCS2D01G591100 chr7A 89.831 118 9 3 2247 2363 227084417 227084532 6.960000e-32 148.0
14 TraesCS2D01G591100 chr7A 91.667 96 4 1 2509 2604 227085564 227085655 2.520000e-26 130.0
15 TraesCS2D01G591100 chr2A 94.459 1877 73 15 563 2411 773199493 773197620 0.000000e+00 2861.0
16 TraesCS2D01G591100 chr2A 94.394 1855 46 19 586 2414 515452120 515453942 0.000000e+00 2796.0
17 TraesCS2D01G591100 chr2A 93.772 289 10 4 252 533 773201051 773200764 7.990000e-116 427.0
18 TraesCS2D01G591100 chr2A 96.761 247 8 0 1 247 256202203 256202449 2.240000e-111 412.0
19 TraesCS2D01G591100 chr2A 84.049 326 36 6 2793 3116 773195318 773195007 1.820000e-77 300.0
20 TraesCS2D01G591100 chr2A 85.333 225 22 4 2418 2639 773197210 773196994 4.040000e-54 222.0
21 TraesCS2D01G591100 chr2A 86.982 169 7 10 2639 2807 773196810 773196657 3.190000e-40 176.0
22 TraesCS2D01G591100 chr2A 81.111 180 6 10 2415 2587 515454809 515454967 5.460000e-23 119.0
23 TraesCS2D01G591100 chr4A 96.787 249 8 0 1 249 729868875 729869123 1.730000e-112 416.0
24 TraesCS2D01G591100 chr7B 96.371 248 9 0 1 248 717329152 717328905 2.890000e-110 409.0
25 TraesCS2D01G591100 chrUn 96.356 247 9 0 1 247 287542522 287542768 1.040000e-109 407.0
26 TraesCS2D01G591100 chr4B 95.652 253 11 0 1 253 40215473 40215221 1.040000e-109 407.0
27 TraesCS2D01G591100 chr4B 89.394 66 5 2 2277 2342 387353317 387353254 7.160000e-12 82.4
28 TraesCS2D01G591100 chr4B 86.957 69 7 2 2274 2342 387353252 387353318 3.330000e-10 76.8
29 TraesCS2D01G591100 chr1A 96.356 247 9 0 1 247 49354381 49354627 1.040000e-109 407.0
30 TraesCS2D01G591100 chr6A 96.000 250 9 1 1 250 584038688 584038440 3.740000e-109 405.0
31 TraesCS2D01G591100 chr3B 88.406 69 3 3 2277 2341 537420599 537420666 9.260000e-11 78.7
32 TraesCS2D01G591100 chr5A 88.060 67 4 2 2277 2343 662382260 662382322 3.330000e-10 76.8
33 TraesCS2D01G591100 chr4D 85.507 69 7 3 2275 2341 444255079 444255146 5.580000e-08 69.4
34 TraesCS2D01G591100 chr3D 85.294 68 9 1 2274 2341 580413115 580413181 5.580000e-08 69.4


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 TraesCS2D01G591100 chr2D 646607562 646610677 3115 False 5755.000000 5755 100.000000 1 3116 1 chr2D.!!$F1 3115
1 TraesCS2D01G591100 chr2D 647232161 647233785 1624 False 2244.000000 2244 92.279000 252 1812 1 chr2D.!!$F2 1560
2 TraesCS2D01G591100 chr2D 646252051 646253140 1089 False 843.000000 1240 94.690500 1037 2278 2 chr2D.!!$F3 1241
3 TraesCS2D01G591100 chr2D 646444323 646445472 1149 True 731.000000 1066 89.533000 970 2284 2 chr2D.!!$R1 1314
4 TraesCS2D01G591100 chr2B 788683634 788686736 3102 True 1321.666667 2915 94.643333 371 3116 3 chr2B.!!$R1 2745
5 TraesCS2D01G591100 chr2B 788988977 788989604 627 False 747.000000 747 88.571000 1634 2245 1 chr2B.!!$F2 611
6 TraesCS2D01G591100 chr7A 227081966 227085655 3689 False 1046.333333 2861 91.142333 254 2604 3 chr7A.!!$F1 2350
7 TraesCS2D01G591100 chr2A 515452120 515454967 2847 False 1457.500000 2796 87.752500 586 2587 2 chr2A.!!$F2 2001
8 TraesCS2D01G591100 chr2A 773195007 773201051 6044 True 797.200000 2861 88.919000 252 3116 5 chr2A.!!$R1 2864

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
156 157 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.0 4.96 0.0 31.08 2.90 F
185 186 0.041663 GTGTGCGTGTGTGCGTTAAT 60.042 50.0 0.00 0.0 37.81 1.40 F
930 2233 0.107263 TTGGTGAACACAGAGCTGCA 60.107 50.0 1.02 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1032 2340 0.534203 GCGACCTCTTTTCACCACCA 60.534 55.0 0.0 0.0 0.00 4.17 R
2017 3339 0.687757 ATCCGCAGCTCTCCCTTGTA 60.688 55.0 0.0 0.0 0.00 2.41 R
2673 6123 0.463654 AGCACCTCACGTTTCTTGCA 60.464 50.0 10.6 0.0 32.24 4.08 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 2.555123 TTCAAATCCTGGTGCTCGC 58.445 52.632 0.00 0.00 0.00 5.03
19 20 0.250684 TTCAAATCCTGGTGCTCGCA 60.251 50.000 0.00 0.00 0.00 5.10
20 21 0.035152 TCAAATCCTGGTGCTCGCAT 60.035 50.000 0.00 0.00 0.00 4.73
21 22 0.813184 CAAATCCTGGTGCTCGCATT 59.187 50.000 0.00 0.00 0.00 3.56
22 23 2.016318 CAAATCCTGGTGCTCGCATTA 58.984 47.619 0.00 0.00 0.00 1.90
23 24 2.620115 CAAATCCTGGTGCTCGCATTAT 59.380 45.455 0.00 0.00 0.00 1.28
24 25 2.645838 ATCCTGGTGCTCGCATTATT 57.354 45.000 0.00 0.00 0.00 1.40
25 26 1.953559 TCCTGGTGCTCGCATTATTC 58.046 50.000 0.00 0.00 0.00 1.75
26 27 0.947244 CCTGGTGCTCGCATTATTCC 59.053 55.000 0.00 0.00 0.00 3.01
27 28 1.475751 CCTGGTGCTCGCATTATTCCT 60.476 52.381 0.00 0.00 0.00 3.36
28 29 1.600957 CTGGTGCTCGCATTATTCCTG 59.399 52.381 0.00 0.00 0.00 3.86
29 30 0.947244 GGTGCTCGCATTATTCCTGG 59.053 55.000 0.00 0.00 0.00 4.45
30 31 1.475034 GGTGCTCGCATTATTCCTGGA 60.475 52.381 0.00 0.00 0.00 3.86
31 32 2.498167 GTGCTCGCATTATTCCTGGAT 58.502 47.619 0.00 0.00 0.00 3.41
32 33 2.880890 GTGCTCGCATTATTCCTGGATT 59.119 45.455 0.00 0.00 0.00 3.01
33 34 3.316308 GTGCTCGCATTATTCCTGGATTT 59.684 43.478 0.00 0.00 0.00 2.17
34 35 4.515191 GTGCTCGCATTATTCCTGGATTTA 59.485 41.667 0.00 0.00 0.00 1.40
35 36 5.182001 GTGCTCGCATTATTCCTGGATTTAT 59.818 40.000 0.00 0.00 0.00 1.40
36 37 5.769662 TGCTCGCATTATTCCTGGATTTATT 59.230 36.000 0.00 0.00 0.00 1.40
37 38 6.265196 TGCTCGCATTATTCCTGGATTTATTT 59.735 34.615 0.00 0.00 0.00 1.40
38 39 6.803807 GCTCGCATTATTCCTGGATTTATTTC 59.196 38.462 0.00 0.00 0.00 2.17
39 40 7.522073 GCTCGCATTATTCCTGGATTTATTTCA 60.522 37.037 0.00 0.00 0.00 2.69
40 41 7.874940 TCGCATTATTCCTGGATTTATTTCAG 58.125 34.615 0.00 0.00 0.00 3.02
41 42 7.040478 TCGCATTATTCCTGGATTTATTTCAGG 60.040 37.037 0.00 0.00 46.91 3.86
49 50 6.076981 CTGGATTTATTTCAGGATTTCCGG 57.923 41.667 0.00 0.00 42.08 5.14
50 51 4.340950 TGGATTTATTTCAGGATTTCCGGC 59.659 41.667 0.00 0.00 42.08 6.13
51 52 4.537015 GATTTATTTCAGGATTTCCGGCG 58.463 43.478 0.00 0.00 42.08 6.46
52 53 2.992124 TATTTCAGGATTTCCGGCGA 57.008 45.000 9.30 0.00 42.08 5.54
53 54 2.348411 ATTTCAGGATTTCCGGCGAT 57.652 45.000 9.30 0.00 42.08 4.58
54 55 1.378531 TTTCAGGATTTCCGGCGATG 58.621 50.000 9.30 0.00 42.08 3.84
55 56 1.095228 TTCAGGATTTCCGGCGATGC 61.095 55.000 9.30 0.00 42.08 3.91
56 57 2.588877 AGGATTTCCGGCGATGCG 60.589 61.111 9.30 0.00 42.08 4.73
67 68 2.787249 CGATGCGCTTTCAGTGGG 59.213 61.111 9.73 0.00 0.00 4.61
68 69 1.741401 CGATGCGCTTTCAGTGGGA 60.741 57.895 9.73 0.00 0.00 4.37
69 70 1.699656 CGATGCGCTTTCAGTGGGAG 61.700 60.000 9.73 0.00 0.00 4.30
70 71 1.372087 GATGCGCTTTCAGTGGGAGG 61.372 60.000 9.73 0.00 0.00 4.30
71 72 1.841302 ATGCGCTTTCAGTGGGAGGA 61.841 55.000 9.73 0.00 0.00 3.71
72 73 1.743252 GCGCTTTCAGTGGGAGGAG 60.743 63.158 0.00 0.00 0.00 3.69
73 74 1.975327 CGCTTTCAGTGGGAGGAGA 59.025 57.895 0.00 0.00 0.00 3.71
74 75 0.539051 CGCTTTCAGTGGGAGGAGAT 59.461 55.000 0.00 0.00 0.00 2.75
75 76 1.741732 CGCTTTCAGTGGGAGGAGATG 60.742 57.143 0.00 0.00 0.00 2.90
76 77 1.280421 GCTTTCAGTGGGAGGAGATGT 59.720 52.381 0.00 0.00 0.00 3.06
77 78 2.290577 GCTTTCAGTGGGAGGAGATGTT 60.291 50.000 0.00 0.00 0.00 2.71
78 79 3.604582 CTTTCAGTGGGAGGAGATGTTC 58.395 50.000 0.00 0.00 0.00 3.18
87 88 2.750815 GGAGATGTTCCCGTTGACG 58.249 57.895 0.00 0.00 40.37 4.35
88 89 0.245539 GGAGATGTTCCCGTTGACGA 59.754 55.000 4.91 0.00 40.37 4.20
89 90 1.347320 GAGATGTTCCCGTTGACGAC 58.653 55.000 4.91 0.00 43.02 4.34
98 99 4.719369 GTTGACGACGAGGCGCCT 62.719 66.667 33.48 33.48 33.86 5.52
99 100 3.057548 TTGACGACGAGGCGCCTA 61.058 61.111 32.97 9.31 33.86 3.93
100 101 3.332493 TTGACGACGAGGCGCCTAC 62.332 63.158 32.97 22.05 33.86 3.18
101 102 4.883300 GACGACGAGGCGCCTACG 62.883 72.222 32.91 32.91 44.07 3.51
104 105 4.849329 GACGAGGCGCCTACGGTG 62.849 72.222 34.97 23.88 40.57 4.94
106 107 4.554363 CGAGGCGCCTACGGTGAG 62.554 72.222 32.97 10.97 40.57 3.51
107 108 3.450115 GAGGCGCCTACGGTGAGT 61.450 66.667 32.97 3.02 40.57 3.41
108 109 2.995574 AGGCGCCTACGGTGAGTT 60.996 61.111 31.86 0.00 40.57 3.01
109 110 2.508663 GGCGCCTACGGTGAGTTC 60.509 66.667 22.15 0.00 40.57 3.01
110 111 2.879462 GCGCCTACGGTGAGTTCG 60.879 66.667 0.00 0.00 40.57 3.95
111 112 2.564975 CGCCTACGGTGAGTTCGT 59.435 61.111 0.00 0.00 43.64 3.85
112 113 1.796151 CGCCTACGGTGAGTTCGTA 59.204 57.895 0.00 0.00 41.38 3.43
113 114 0.168788 CGCCTACGGTGAGTTCGTAA 59.831 55.000 0.00 0.00 41.62 3.18
114 115 1.401409 CGCCTACGGTGAGTTCGTAAA 60.401 52.381 0.00 0.00 41.62 2.01
115 116 2.733227 CGCCTACGGTGAGTTCGTAAAT 60.733 50.000 0.00 0.00 41.62 1.40
116 117 2.856557 GCCTACGGTGAGTTCGTAAATC 59.143 50.000 0.00 0.00 41.62 2.17
117 118 3.428589 GCCTACGGTGAGTTCGTAAATCT 60.429 47.826 0.00 0.00 41.62 2.40
118 119 4.349501 CCTACGGTGAGTTCGTAAATCTC 58.650 47.826 0.00 0.00 41.62 2.75
119 120 3.928727 ACGGTGAGTTCGTAAATCTCA 57.071 42.857 0.00 0.00 39.22 3.27
120 121 4.247267 ACGGTGAGTTCGTAAATCTCAA 57.753 40.909 0.00 0.00 39.42 3.02
121 122 4.235360 ACGGTGAGTTCGTAAATCTCAAG 58.765 43.478 0.00 0.00 39.42 3.02
122 123 4.022589 ACGGTGAGTTCGTAAATCTCAAGA 60.023 41.667 0.00 0.00 39.42 3.02
123 124 5.103000 CGGTGAGTTCGTAAATCTCAAGAT 58.897 41.667 0.00 0.00 39.42 2.40
124 125 6.127814 ACGGTGAGTTCGTAAATCTCAAGATA 60.128 38.462 0.00 0.00 39.42 1.98
125 126 6.750501 CGGTGAGTTCGTAAATCTCAAGATAA 59.249 38.462 0.00 0.00 39.42 1.75
126 127 7.435488 CGGTGAGTTCGTAAATCTCAAGATAAT 59.565 37.037 0.00 0.00 39.42 1.28
127 128 9.745880 GGTGAGTTCGTAAATCTCAAGATAATA 57.254 33.333 0.00 0.00 39.42 0.98
131 132 9.209175 AGTTCGTAAATCTCAAGATAATATGCC 57.791 33.333 0.00 0.00 33.73 4.40
132 133 8.988934 GTTCGTAAATCTCAAGATAATATGCCA 58.011 33.333 0.00 0.00 33.73 4.92
133 134 8.763049 TCGTAAATCTCAAGATAATATGCCAG 57.237 34.615 0.00 0.00 33.73 4.85
134 135 7.331934 TCGTAAATCTCAAGATAATATGCCAGC 59.668 37.037 0.00 0.00 33.73 4.85
135 136 7.332926 CGTAAATCTCAAGATAATATGCCAGCT 59.667 37.037 0.00 0.00 33.73 4.24
136 137 7.684937 AAATCTCAAGATAATATGCCAGCTC 57.315 36.000 0.00 0.00 33.73 4.09
137 138 5.813513 TCTCAAGATAATATGCCAGCTCA 57.186 39.130 0.00 0.00 0.00 4.26
138 139 5.791666 TCTCAAGATAATATGCCAGCTCAG 58.208 41.667 0.00 0.00 0.00 3.35
139 140 5.306419 TCTCAAGATAATATGCCAGCTCAGT 59.694 40.000 0.00 0.00 0.00 3.41
140 141 5.545588 TCAAGATAATATGCCAGCTCAGTC 58.454 41.667 0.00 0.00 0.00 3.51
141 142 5.306419 TCAAGATAATATGCCAGCTCAGTCT 59.694 40.000 0.00 0.00 0.00 3.24
142 143 5.404466 AGATAATATGCCAGCTCAGTCTC 57.596 43.478 0.00 0.00 0.00 3.36
143 144 5.085920 AGATAATATGCCAGCTCAGTCTCT 58.914 41.667 0.00 0.00 0.00 3.10
144 145 3.749665 AATATGCCAGCTCAGTCTCTC 57.250 47.619 0.00 0.00 0.00 3.20
145 146 1.028130 TATGCCAGCTCAGTCTCTCG 58.972 55.000 0.00 0.00 0.00 4.04
146 147 1.674764 ATGCCAGCTCAGTCTCTCGG 61.675 60.000 0.00 0.00 0.00 4.63
147 148 2.049185 GCCAGCTCAGTCTCTCGGA 61.049 63.158 0.00 0.00 0.00 4.55
148 149 2.003658 GCCAGCTCAGTCTCTCGGAG 62.004 65.000 0.00 0.00 40.44 4.63
149 150 1.383456 CCAGCTCAGTCTCTCGGAGG 61.383 65.000 4.96 0.00 38.48 4.30
150 151 0.679640 CAGCTCAGTCTCTCGGAGGT 60.680 60.000 4.96 0.00 46.44 3.85
151 152 0.679640 AGCTCAGTCTCTCGGAGGTG 60.680 60.000 4.96 0.00 44.55 4.00
152 153 1.806568 CTCAGTCTCTCGGAGGTGC 59.193 63.158 4.96 0.00 35.32 5.01
153 154 0.679640 CTCAGTCTCTCGGAGGTGCT 60.680 60.000 4.96 0.00 35.32 4.40
154 155 0.678366 TCAGTCTCTCGGAGGTGCTC 60.678 60.000 4.96 0.00 0.00 4.26
155 156 0.962855 CAGTCTCTCGGAGGTGCTCA 60.963 60.000 4.96 0.00 31.08 4.26
156 157 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.000 4.96 0.00 31.08 2.90
157 158 1.213182 AGTCTCTCGGAGGTGCTCATA 59.787 52.381 4.96 0.00 31.08 2.15
158 159 1.606668 GTCTCTCGGAGGTGCTCATAG 59.393 57.143 4.96 0.00 31.08 2.23
159 160 0.958091 CTCTCGGAGGTGCTCATAGG 59.042 60.000 4.96 0.00 31.08 2.57
160 161 0.468214 TCTCGGAGGTGCTCATAGGG 60.468 60.000 4.96 0.00 31.08 3.53
161 162 1.457643 TCGGAGGTGCTCATAGGGG 60.458 63.158 0.00 0.00 31.08 4.79
162 163 1.762460 CGGAGGTGCTCATAGGGGT 60.762 63.158 0.00 0.00 31.08 4.95
163 164 0.469331 CGGAGGTGCTCATAGGGGTA 60.469 60.000 0.00 0.00 31.08 3.69
164 165 1.343069 GGAGGTGCTCATAGGGGTAG 58.657 60.000 0.00 0.00 31.08 3.18
165 166 1.343069 GAGGTGCTCATAGGGGTAGG 58.657 60.000 0.00 0.00 0.00 3.18
166 167 0.104934 AGGTGCTCATAGGGGTAGGG 60.105 60.000 0.00 0.00 0.00 3.53
167 168 0.400093 GGTGCTCATAGGGGTAGGGT 60.400 60.000 0.00 0.00 0.00 4.34
168 169 0.759346 GTGCTCATAGGGGTAGGGTG 59.241 60.000 0.00 0.00 0.00 4.61
169 170 0.341961 TGCTCATAGGGGTAGGGTGT 59.658 55.000 0.00 0.00 0.00 4.16
170 171 0.759346 GCTCATAGGGGTAGGGTGTG 59.241 60.000 0.00 0.00 0.00 3.82
171 172 0.759346 CTCATAGGGGTAGGGTGTGC 59.241 60.000 0.00 0.00 0.00 4.57
172 173 1.046472 TCATAGGGGTAGGGTGTGCG 61.046 60.000 0.00 0.00 0.00 5.34
173 174 1.002533 ATAGGGGTAGGGTGTGCGT 59.997 57.895 0.00 0.00 0.00 5.24
174 175 1.335132 ATAGGGGTAGGGTGTGCGTG 61.335 60.000 0.00 0.00 0.00 5.34
175 176 2.735151 TAGGGGTAGGGTGTGCGTGT 62.735 60.000 0.00 0.00 0.00 4.49
176 177 2.358247 GGGTAGGGTGTGCGTGTG 60.358 66.667 0.00 0.00 0.00 3.82
177 178 2.424302 GGTAGGGTGTGCGTGTGT 59.576 61.111 0.00 0.00 0.00 3.72
178 179 1.959226 GGTAGGGTGTGCGTGTGTG 60.959 63.158 0.00 0.00 0.00 3.82
179 180 2.280524 TAGGGTGTGCGTGTGTGC 60.281 61.111 0.00 0.00 0.00 4.57
182 183 3.871574 GGTGTGCGTGTGTGCGTT 61.872 61.111 0.00 0.00 37.81 4.84
183 184 2.526993 GGTGTGCGTGTGTGCGTTA 61.527 57.895 0.00 0.00 37.81 3.18
184 185 1.348938 GTGTGCGTGTGTGCGTTAA 59.651 52.632 0.00 0.00 37.81 2.01
185 186 0.041663 GTGTGCGTGTGTGCGTTAAT 60.042 50.000 0.00 0.00 37.81 1.40
186 187 1.192757 GTGTGCGTGTGTGCGTTAATA 59.807 47.619 0.00 0.00 37.81 0.98
187 188 1.457683 TGTGCGTGTGTGCGTTAATAG 59.542 47.619 0.00 0.00 37.81 1.73
188 189 1.072391 TGCGTGTGTGCGTTAATAGG 58.928 50.000 0.00 0.00 37.81 2.57
189 190 0.372334 GCGTGTGTGCGTTAATAGGG 59.628 55.000 0.00 0.00 0.00 3.53
190 191 1.999048 CGTGTGTGCGTTAATAGGGA 58.001 50.000 0.00 0.00 0.00 4.20
191 192 2.546778 CGTGTGTGCGTTAATAGGGAT 58.453 47.619 0.00 0.00 0.00 3.85
192 193 2.284150 CGTGTGTGCGTTAATAGGGATG 59.716 50.000 0.00 0.00 0.00 3.51
193 194 3.527533 GTGTGTGCGTTAATAGGGATGA 58.472 45.455 0.00 0.00 0.00 2.92
194 195 3.555956 GTGTGTGCGTTAATAGGGATGAG 59.444 47.826 0.00 0.00 0.00 2.90
195 196 3.196901 TGTGTGCGTTAATAGGGATGAGT 59.803 43.478 0.00 0.00 0.00 3.41
196 197 3.555956 GTGTGCGTTAATAGGGATGAGTG 59.444 47.826 0.00 0.00 0.00 3.51
197 198 3.196901 TGTGCGTTAATAGGGATGAGTGT 59.803 43.478 0.00 0.00 0.00 3.55
198 199 4.403113 TGTGCGTTAATAGGGATGAGTGTA 59.597 41.667 0.00 0.00 0.00 2.90
199 200 5.069914 TGTGCGTTAATAGGGATGAGTGTAT 59.930 40.000 0.00 0.00 0.00 2.29
200 201 5.405571 GTGCGTTAATAGGGATGAGTGTATG 59.594 44.000 0.00 0.00 0.00 2.39
201 202 4.389077 GCGTTAATAGGGATGAGTGTATGC 59.611 45.833 0.00 0.00 0.00 3.14
202 203 4.621460 CGTTAATAGGGATGAGTGTATGCG 59.379 45.833 0.00 0.00 0.00 4.73
203 204 2.751166 ATAGGGATGAGTGTATGCGC 57.249 50.000 0.00 0.00 0.00 6.09
204 205 0.313987 TAGGGATGAGTGTATGCGCG 59.686 55.000 0.00 0.00 0.00 6.86
205 206 1.227263 GGGATGAGTGTATGCGCGT 60.227 57.895 8.43 7.55 0.00 6.01
206 207 1.490693 GGGATGAGTGTATGCGCGTG 61.491 60.000 13.61 0.00 0.00 5.34
207 208 0.806102 GGATGAGTGTATGCGCGTGT 60.806 55.000 13.61 0.00 0.00 4.49
208 209 1.535226 GGATGAGTGTATGCGCGTGTA 60.535 52.381 13.61 0.00 0.00 2.90
209 210 2.394708 GATGAGTGTATGCGCGTGTAT 58.605 47.619 13.61 4.63 0.00 2.29
210 211 3.561503 GATGAGTGTATGCGCGTGTATA 58.438 45.455 13.61 2.40 0.00 1.47
211 212 3.636282 TGAGTGTATGCGCGTGTATAT 57.364 42.857 13.61 0.00 0.00 0.86
212 213 3.305110 TGAGTGTATGCGCGTGTATATG 58.695 45.455 13.61 0.00 0.00 1.78
213 214 3.003897 TGAGTGTATGCGCGTGTATATGA 59.996 43.478 13.61 0.00 0.00 2.15
214 215 3.565516 AGTGTATGCGCGTGTATATGAG 58.434 45.455 13.61 0.00 0.00 2.90
215 216 2.090658 GTGTATGCGCGTGTATATGAGC 59.909 50.000 13.61 0.41 38.85 4.26
218 219 4.228451 CGCGTGTATATGAGCGCT 57.772 55.556 11.27 11.27 46.56 5.92
219 220 2.506544 CGCGTGTATATGAGCGCTT 58.493 52.632 13.26 0.00 46.56 4.68
220 221 0.159554 CGCGTGTATATGAGCGCTTG 59.840 55.000 13.26 0.00 46.56 4.01
221 222 1.209128 GCGTGTATATGAGCGCTTGT 58.791 50.000 13.26 5.98 45.48 3.16
222 223 1.071239 GCGTGTATATGAGCGCTTGTG 60.071 52.381 13.26 0.00 45.48 3.33
223 224 2.193447 CGTGTATATGAGCGCTTGTGT 58.807 47.619 13.26 4.27 0.00 3.72
224 225 2.603110 CGTGTATATGAGCGCTTGTGTT 59.397 45.455 13.26 0.00 0.00 3.32
225 226 3.062099 CGTGTATATGAGCGCTTGTGTTT 59.938 43.478 13.26 0.00 0.00 2.83
226 227 4.334443 GTGTATATGAGCGCTTGTGTTTG 58.666 43.478 13.26 0.00 0.00 2.93
227 228 4.000325 TGTATATGAGCGCTTGTGTTTGT 59.000 39.130 13.26 0.00 0.00 2.83
228 229 5.062934 GTGTATATGAGCGCTTGTGTTTGTA 59.937 40.000 13.26 0.00 0.00 2.41
229 230 2.969443 ATGAGCGCTTGTGTTTGTAC 57.031 45.000 13.26 0.00 0.00 2.90
230 231 1.948104 TGAGCGCTTGTGTTTGTACT 58.052 45.000 13.26 0.00 0.00 2.73
231 232 1.597195 TGAGCGCTTGTGTTTGTACTG 59.403 47.619 13.26 0.00 0.00 2.74
232 233 1.864711 GAGCGCTTGTGTTTGTACTGA 59.135 47.619 13.26 0.00 0.00 3.41
233 234 2.480419 GAGCGCTTGTGTTTGTACTGAT 59.520 45.455 13.26 0.00 0.00 2.90
234 235 2.224079 AGCGCTTGTGTTTGTACTGATG 59.776 45.455 2.64 0.00 0.00 3.07
235 236 2.574322 CGCTTGTGTTTGTACTGATGC 58.426 47.619 0.00 0.00 0.00 3.91
236 237 2.224079 CGCTTGTGTTTGTACTGATGCT 59.776 45.455 0.00 0.00 0.00 3.79
237 238 3.665323 CGCTTGTGTTTGTACTGATGCTC 60.665 47.826 0.00 0.00 0.00 4.26
238 239 3.250762 GCTTGTGTTTGTACTGATGCTCA 59.749 43.478 0.00 0.00 0.00 4.26
239 240 4.261155 GCTTGTGTTTGTACTGATGCTCAA 60.261 41.667 0.00 0.00 0.00 3.02
240 241 5.733091 GCTTGTGTTTGTACTGATGCTCAAA 60.733 40.000 0.00 0.00 0.00 2.69
241 242 5.826601 TGTGTTTGTACTGATGCTCAAAA 57.173 34.783 0.00 0.00 32.81 2.44
242 243 6.201226 TGTGTTTGTACTGATGCTCAAAAA 57.799 33.333 0.00 0.00 32.81 1.94
282 288 1.669115 CTGACGGCTCCACACTTGG 60.669 63.158 0.00 0.00 45.56 3.61
422 451 3.989595 GATTAGCGAGCGCACGGC 61.990 66.667 27.65 19.21 44.88 5.68
474 513 5.515626 CGTCCACGAATACTTTTCTCCTAAG 59.484 44.000 0.00 0.00 43.02 2.18
493 532 7.582719 TCCTAAGAAAACACCAGCCATATATT 58.417 34.615 0.00 0.00 0.00 1.28
553 1820 4.514577 CGCCGCCGGACTGATTCT 62.515 66.667 7.68 0.00 0.00 2.40
554 1821 2.125106 GCCGCCGGACTGATTCTT 60.125 61.111 7.68 0.00 0.00 2.52
556 1823 1.815421 CCGCCGGACTGATTCTTGG 60.815 63.158 5.05 0.00 0.00 3.61
560 1841 0.179000 CCGGACTGATTCTTGGAGGG 59.821 60.000 0.00 0.00 0.00 4.30
561 1842 0.905357 CGGACTGATTCTTGGAGGGT 59.095 55.000 0.00 0.00 0.00 4.34
574 1855 1.377202 GAGGGTTGATTCTGGCGCA 60.377 57.895 10.83 0.00 0.00 6.09
580 1861 2.746277 GATTCTGGCGCACCGGTT 60.746 61.111 2.97 0.00 43.58 4.44
593 1874 2.342279 CGGTTTGACGGAGAGGCA 59.658 61.111 0.00 0.00 34.88 4.75
597 1878 3.885814 TTGACGGAGAGGCAAGGT 58.114 55.556 0.00 0.00 44.35 3.50
628 1909 1.995542 AGGGTGTGGATTGAATCTGGT 59.004 47.619 5.03 0.00 0.00 4.00
658 1939 3.470888 CCCCGATTCGCCCTCACT 61.471 66.667 0.00 0.00 0.00 3.41
678 1959 3.330720 AGGCAGGGCAGGTACACC 61.331 66.667 0.00 0.00 0.00 4.16
679 1960 3.646715 GGCAGGGCAGGTACACCA 61.647 66.667 0.38 0.00 38.89 4.17
816 2102 1.394151 CAACTCCTCCCCTCCCTCT 59.606 63.158 0.00 0.00 0.00 3.69
822 2108 1.944588 TCCTCCCCTCCCTCTAATTCA 59.055 52.381 0.00 0.00 0.00 2.57
876 2176 3.491447 GCGGCATCATAAATTCAAGGCTT 60.491 43.478 0.00 0.00 0.00 4.35
877 2177 4.293415 CGGCATCATAAATTCAAGGCTTC 58.707 43.478 0.00 0.00 0.00 3.86
908 2208 1.721926 CGAAACTCTTCAAGGACGCTC 59.278 52.381 0.00 0.00 0.00 5.03
926 2226 1.728971 CTCGATTGGTGAACACAGAGC 59.271 52.381 7.25 0.00 0.00 4.09
927 2227 1.344438 TCGATTGGTGAACACAGAGCT 59.656 47.619 7.25 0.00 0.00 4.09
930 2233 0.107263 TTGGTGAACACAGAGCTGCA 60.107 50.000 1.02 0.00 0.00 4.41
935 2238 1.575576 GAACACAGAGCTGCAGCAGG 61.576 60.000 38.24 27.68 45.16 4.85
941 2244 2.284478 AGCTGCAGCAGGAGGAGA 60.284 61.111 38.24 0.00 45.16 3.71
943 2246 1.224039 GCTGCAGCAGGAGGAGAAT 59.776 57.895 33.36 0.00 41.59 2.40
944 2247 0.394080 GCTGCAGCAGGAGGAGAATT 60.394 55.000 33.36 0.00 41.59 2.17
1035 2343 4.856801 GGACATGCCGGCGATGGT 62.857 66.667 29.78 22.09 0.00 3.55
2017 3339 5.981174 CCATATTTGGGCTCAAGTTCAATT 58.019 37.500 0.00 0.00 39.56 2.32
2282 3621 7.097834 GGTATGCTAGTTATTGATGTACTCCC 58.902 42.308 0.00 0.00 0.00 4.30
2284 3623 6.808321 TGCTAGTTATTGATGTACTCCCTT 57.192 37.500 0.00 0.00 0.00 3.95
2290 3629 2.225382 TGATGTACTCCCTTCGTCCA 57.775 50.000 0.00 0.00 0.00 4.02
2414 3816 6.489022 GGTCCTATGGTTGAACAAAACTAACT 59.511 38.462 0.00 0.00 0.00 2.24
2415 3817 7.662669 GGTCCTATGGTTGAACAAAACTAACTA 59.337 37.037 0.00 0.00 0.00 2.24
2551 5817 0.394899 GAAGGATGTGCAAGGGAGGG 60.395 60.000 0.00 0.00 0.00 4.30
2552 5818 0.846427 AAGGATGTGCAAGGGAGGGA 60.846 55.000 0.00 0.00 0.00 4.20
2553 5819 1.225704 GGATGTGCAAGGGAGGGAG 59.774 63.158 0.00 0.00 0.00 4.30
2554 5820 1.225704 GATGTGCAAGGGAGGGAGG 59.774 63.158 0.00 0.00 0.00 4.30
2594 5860 2.095161 AGAAAACACGACAACGGCAAAA 60.095 40.909 0.00 0.00 44.46 2.44
2595 5861 1.619983 AAACACGACAACGGCAAAAC 58.380 45.000 0.00 0.00 44.46 2.43
2625 5891 2.282745 GCCTGCAAAGGAGCCTGT 60.283 61.111 0.00 0.00 0.00 4.00
2671 6121 4.339530 AGGGCAAAAACAAGAGAGAAGAAC 59.660 41.667 0.00 0.00 0.00 3.01
2672 6122 4.097892 GGGCAAAAACAAGAGAGAAGAACA 59.902 41.667 0.00 0.00 0.00 3.18
2673 6123 5.221322 GGGCAAAAACAAGAGAGAAGAACAT 60.221 40.000 0.00 0.00 0.00 2.71
2674 6124 5.689068 GGCAAAAACAAGAGAGAAGAACATG 59.311 40.000 0.00 0.00 0.00 3.21
2675 6125 5.174579 GCAAAAACAAGAGAGAAGAACATGC 59.825 40.000 0.00 0.00 0.00 4.06
2676 6126 6.267817 CAAAAACAAGAGAGAAGAACATGCA 58.732 36.000 0.00 0.00 0.00 3.96
2677 6127 6.455360 AAAACAAGAGAGAAGAACATGCAA 57.545 33.333 0.00 0.00 0.00 4.08
2706 6163 0.035056 GGTGCTTGTAGATGGCAGGT 60.035 55.000 0.00 0.00 36.62 4.00
2825 7634 5.470845 ACTAGCAATATTCACAAGCGAAC 57.529 39.130 0.00 0.00 0.00 3.95
2836 7651 6.895607 TTCACAAGCGAACGAATATGAATA 57.104 33.333 0.00 0.00 0.00 1.75
2837 7652 7.477144 TTCACAAGCGAACGAATATGAATAT 57.523 32.000 0.00 0.00 0.00 1.28
2838 7653 6.876804 TCACAAGCGAACGAATATGAATATG 58.123 36.000 0.00 0.00 0.00 1.78
2839 7654 6.699642 TCACAAGCGAACGAATATGAATATGA 59.300 34.615 0.00 0.00 0.00 2.15
2840 7655 7.223777 TCACAAGCGAACGAATATGAATATGAA 59.776 33.333 0.00 0.00 0.00 2.57
2841 7656 8.011673 CACAAGCGAACGAATATGAATATGAAT 58.988 33.333 0.00 0.00 0.00 2.57
2842 7657 8.223769 ACAAGCGAACGAATATGAATATGAATC 58.776 33.333 0.00 0.00 0.00 2.52
2843 7658 7.889589 AGCGAACGAATATGAATATGAATCA 57.110 32.000 0.00 0.00 0.00 2.57
2844 7659 7.957615 AGCGAACGAATATGAATATGAATCAG 58.042 34.615 0.00 0.00 0.00 2.90
2894 7709 3.406764 AGCCGGAGATTCTATGCATTTC 58.593 45.455 5.05 0.00 0.00 2.17
2916 7731 2.409870 CCTTTGGAGGTCGCCATGC 61.410 63.158 0.00 0.00 37.86 4.06
2917 7732 1.675310 CTTTGGAGGTCGCCATGCA 60.675 57.895 0.00 0.00 37.86 3.96
2918 7733 1.001020 TTTGGAGGTCGCCATGCAT 60.001 52.632 0.00 0.00 37.86 3.96
2919 7734 1.314534 TTTGGAGGTCGCCATGCATG 61.315 55.000 20.19 20.19 37.86 4.06
2961 7776 1.521450 GCGCAGATTAGCCCATGCAT 61.521 55.000 0.30 0.00 41.13 3.96
2963 7778 2.153645 CGCAGATTAGCCCATGCATTA 58.846 47.619 0.00 0.00 41.13 1.90
2980 7795 3.195396 GCATTATGGCCTCAAGGTTGAAA 59.805 43.478 3.32 0.00 36.64 2.69
3006 7821 1.004277 CAGTAGCCCAGCCCTAAACAA 59.996 52.381 0.00 0.00 0.00 2.83
3009 7824 1.076727 GCCCAGCCCTAAACAAGGT 59.923 57.895 0.00 0.00 44.90 3.50
3011 7826 0.112412 CCCAGCCCTAAACAAGGTGT 59.888 55.000 0.00 0.00 44.90 4.16
3012 7827 1.247567 CCAGCCCTAAACAAGGTGTG 58.752 55.000 0.00 0.00 44.90 3.82
3013 7828 0.598065 CAGCCCTAAACAAGGTGTGC 59.402 55.000 0.00 0.00 44.90 4.57
3014 7829 0.478507 AGCCCTAAACAAGGTGTGCT 59.521 50.000 0.00 0.00 44.90 4.40
3015 7830 0.598065 GCCCTAAACAAGGTGTGCTG 59.402 55.000 0.00 0.00 44.90 4.41
3016 7831 1.817740 GCCCTAAACAAGGTGTGCTGA 60.818 52.381 0.00 0.00 44.90 4.26
3017 7832 2.795329 CCCTAAACAAGGTGTGCTGAT 58.205 47.619 0.00 0.00 44.90 2.90
3018 7833 2.489329 CCCTAAACAAGGTGTGCTGATG 59.511 50.000 0.00 0.00 44.90 3.07
3020 7835 0.675633 AAACAAGGTGTGCTGATGGC 59.324 50.000 0.00 0.00 42.22 4.40
3021 7836 1.518056 AACAAGGTGTGCTGATGGCG 61.518 55.000 0.00 0.00 45.43 5.69
3022 7837 1.968017 CAAGGTGTGCTGATGGCGT 60.968 57.895 0.00 0.00 45.43 5.68
3024 7839 4.107051 GGTGTGCTGATGGCGTGC 62.107 66.667 0.00 0.00 45.43 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.813184 AATGCGAGCACCAGGATTTG 59.187 50.000 0.00 0.00 0.00 2.32
3 4 2.418368 TAATGCGAGCACCAGGATTT 57.582 45.000 0.00 0.00 31.11 2.17
5 6 2.498167 GAATAATGCGAGCACCAGGAT 58.502 47.619 0.00 0.00 0.00 3.24
6 7 1.475034 GGAATAATGCGAGCACCAGGA 60.475 52.381 0.00 0.00 0.00 3.86
7 8 0.947244 GGAATAATGCGAGCACCAGG 59.053 55.000 0.00 0.00 0.00 4.45
8 9 1.600957 CAGGAATAATGCGAGCACCAG 59.399 52.381 0.00 0.00 0.00 4.00
9 10 1.667236 CAGGAATAATGCGAGCACCA 58.333 50.000 0.00 0.00 0.00 4.17
10 11 0.947244 CCAGGAATAATGCGAGCACC 59.053 55.000 0.00 0.00 0.00 5.01
11 12 1.953559 TCCAGGAATAATGCGAGCAC 58.046 50.000 0.00 0.00 0.00 4.40
12 13 2.936919 ATCCAGGAATAATGCGAGCA 57.063 45.000 0.00 0.00 0.00 4.26
13 14 5.886960 ATAAATCCAGGAATAATGCGAGC 57.113 39.130 0.00 0.00 0.00 5.03
14 15 7.874940 TGAAATAAATCCAGGAATAATGCGAG 58.125 34.615 0.00 0.00 0.00 5.03
15 16 7.815840 TGAAATAAATCCAGGAATAATGCGA 57.184 32.000 0.00 0.00 0.00 5.10
25 26 5.010012 CCGGAAATCCTGAAATAAATCCAGG 59.990 44.000 0.00 0.00 46.64 4.45
26 27 5.507985 GCCGGAAATCCTGAAATAAATCCAG 60.508 44.000 5.05 0.00 0.00 3.86
27 28 4.340950 GCCGGAAATCCTGAAATAAATCCA 59.659 41.667 5.05 0.00 0.00 3.41
28 29 4.556699 CGCCGGAAATCCTGAAATAAATCC 60.557 45.833 5.05 0.00 0.00 3.01
29 30 4.274950 TCGCCGGAAATCCTGAAATAAATC 59.725 41.667 5.05 0.00 0.00 2.17
30 31 4.204012 TCGCCGGAAATCCTGAAATAAAT 58.796 39.130 5.05 0.00 0.00 1.40
31 32 3.611970 TCGCCGGAAATCCTGAAATAAA 58.388 40.909 5.05 0.00 0.00 1.40
32 33 3.269538 TCGCCGGAAATCCTGAAATAA 57.730 42.857 5.05 0.00 0.00 1.40
33 34 2.992124 TCGCCGGAAATCCTGAAATA 57.008 45.000 5.05 0.00 0.00 1.40
34 35 1.949525 CATCGCCGGAAATCCTGAAAT 59.050 47.619 5.05 0.00 0.00 2.17
35 36 1.378531 CATCGCCGGAAATCCTGAAA 58.621 50.000 5.05 0.00 0.00 2.69
36 37 1.095228 GCATCGCCGGAAATCCTGAA 61.095 55.000 5.05 0.00 0.00 3.02
37 38 1.523711 GCATCGCCGGAAATCCTGA 60.524 57.895 5.05 0.00 0.00 3.86
38 39 2.885676 CGCATCGCCGGAAATCCTG 61.886 63.158 5.05 0.00 0.00 3.86
39 40 2.588877 CGCATCGCCGGAAATCCT 60.589 61.111 5.05 0.00 0.00 3.24
50 51 1.699656 CTCCCACTGAAAGCGCATCG 61.700 60.000 11.47 6.82 37.60 3.84
51 52 1.372087 CCTCCCACTGAAAGCGCATC 61.372 60.000 11.47 8.39 37.60 3.91
52 53 1.377725 CCTCCCACTGAAAGCGCAT 60.378 57.895 11.47 0.00 37.60 4.73
53 54 2.032528 CCTCCCACTGAAAGCGCA 59.967 61.111 11.47 0.00 37.60 6.09
54 55 1.743252 CTCCTCCCACTGAAAGCGC 60.743 63.158 0.00 0.00 37.60 5.92
55 56 0.539051 ATCTCCTCCCACTGAAAGCG 59.461 55.000 0.00 0.00 37.60 4.68
56 57 1.280421 ACATCTCCTCCCACTGAAAGC 59.720 52.381 0.00 0.00 37.60 3.51
57 58 3.604582 GAACATCTCCTCCCACTGAAAG 58.395 50.000 0.00 0.00 42.29 2.62
58 59 2.305927 GGAACATCTCCTCCCACTGAAA 59.694 50.000 0.00 0.00 41.61 2.69
59 60 1.909302 GGAACATCTCCTCCCACTGAA 59.091 52.381 0.00 0.00 41.61 3.02
60 61 1.573108 GGAACATCTCCTCCCACTGA 58.427 55.000 0.00 0.00 41.61 3.41
65 66 0.107654 CAACGGGAACATCTCCTCCC 60.108 60.000 0.00 0.00 46.97 4.30
66 67 0.902531 TCAACGGGAACATCTCCTCC 59.097 55.000 0.00 0.00 44.68 4.30
67 68 1.736032 CGTCAACGGGAACATCTCCTC 60.736 57.143 0.00 0.00 44.68 3.71
68 69 0.246635 CGTCAACGGGAACATCTCCT 59.753 55.000 0.00 0.00 44.68 3.69
69 70 0.245539 TCGTCAACGGGAACATCTCC 59.754 55.000 2.31 0.00 44.54 3.71
70 71 1.347320 GTCGTCAACGGGAACATCTC 58.653 55.000 2.31 0.00 40.29 2.75
71 72 3.509388 GTCGTCAACGGGAACATCT 57.491 52.632 2.31 0.00 40.29 2.90
81 82 3.332493 TAGGCGCCTCGTCGTCAAC 62.332 63.158 36.73 0.00 36.23 3.18
82 83 3.057548 TAGGCGCCTCGTCGTCAA 61.058 61.111 36.73 10.36 36.23 3.18
83 84 3.807538 GTAGGCGCCTCGTCGTCA 61.808 66.667 36.73 11.30 36.23 4.35
84 85 4.883300 CGTAGGCGCCTCGTCGTC 62.883 72.222 36.73 15.88 36.23 4.20
97 98 4.978186 TGAGATTTACGAACTCACCGTAG 58.022 43.478 0.00 0.00 42.42 3.51
98 99 5.181811 TCTTGAGATTTACGAACTCACCGTA 59.818 40.000 0.00 0.00 39.80 4.02
99 100 3.928727 TGAGATTTACGAACTCACCGT 57.071 42.857 0.00 0.00 43.26 4.83
100 101 4.482386 TCTTGAGATTTACGAACTCACCG 58.518 43.478 0.00 0.00 39.80 4.94
101 102 8.649973 ATTATCTTGAGATTTACGAACTCACC 57.350 34.615 0.00 0.00 39.80 4.02
105 106 9.209175 GGCATATTATCTTGAGATTTACGAACT 57.791 33.333 0.00 0.00 36.05 3.01
106 107 8.988934 TGGCATATTATCTTGAGATTTACGAAC 58.011 33.333 0.00 0.00 36.05 3.95
107 108 9.208022 CTGGCATATTATCTTGAGATTTACGAA 57.792 33.333 0.00 0.00 36.05 3.85
108 109 7.331934 GCTGGCATATTATCTTGAGATTTACGA 59.668 37.037 0.00 0.00 36.05 3.43
109 110 7.332926 AGCTGGCATATTATCTTGAGATTTACG 59.667 37.037 0.00 0.00 36.05 3.18
110 111 8.558973 AGCTGGCATATTATCTTGAGATTTAC 57.441 34.615 0.00 0.00 36.05 2.01
111 112 8.377799 TGAGCTGGCATATTATCTTGAGATTTA 58.622 33.333 0.00 0.00 36.05 1.40
112 113 7.229308 TGAGCTGGCATATTATCTTGAGATTT 58.771 34.615 0.00 0.00 36.05 2.17
113 114 6.776744 TGAGCTGGCATATTATCTTGAGATT 58.223 36.000 0.00 0.00 36.05 2.40
114 115 6.013553 ACTGAGCTGGCATATTATCTTGAGAT 60.014 38.462 0.00 0.00 38.51 2.75
115 116 5.306419 ACTGAGCTGGCATATTATCTTGAGA 59.694 40.000 0.00 0.00 0.00 3.27
116 117 5.549347 ACTGAGCTGGCATATTATCTTGAG 58.451 41.667 0.00 0.00 0.00 3.02
117 118 5.306419 AGACTGAGCTGGCATATTATCTTGA 59.694 40.000 0.00 0.00 0.00 3.02
118 119 5.549347 AGACTGAGCTGGCATATTATCTTG 58.451 41.667 0.00 0.00 0.00 3.02
119 120 5.543405 AGAGACTGAGCTGGCATATTATCTT 59.457 40.000 0.00 0.00 0.00 2.40
120 121 5.085920 AGAGACTGAGCTGGCATATTATCT 58.914 41.667 0.00 0.00 0.00 1.98
121 122 5.404466 AGAGACTGAGCTGGCATATTATC 57.596 43.478 0.00 0.00 0.00 1.75
122 123 4.082300 CGAGAGACTGAGCTGGCATATTAT 60.082 45.833 0.00 0.00 0.00 1.28
123 124 3.254411 CGAGAGACTGAGCTGGCATATTA 59.746 47.826 0.00 0.00 0.00 0.98
124 125 2.035704 CGAGAGACTGAGCTGGCATATT 59.964 50.000 0.00 0.00 0.00 1.28
125 126 1.612950 CGAGAGACTGAGCTGGCATAT 59.387 52.381 0.00 0.00 0.00 1.78
126 127 1.028130 CGAGAGACTGAGCTGGCATA 58.972 55.000 0.00 0.00 0.00 3.14
127 128 1.674764 CCGAGAGACTGAGCTGGCAT 61.675 60.000 0.00 0.00 0.00 4.40
128 129 2.346541 CCGAGAGACTGAGCTGGCA 61.347 63.158 0.00 0.00 0.00 4.92
129 130 2.003658 CTCCGAGAGACTGAGCTGGC 62.004 65.000 0.00 0.00 0.00 4.85
130 131 1.383456 CCTCCGAGAGACTGAGCTGG 61.383 65.000 0.00 0.00 0.00 4.85
131 132 0.679640 ACCTCCGAGAGACTGAGCTG 60.680 60.000 0.00 0.00 0.00 4.24
132 133 0.679640 CACCTCCGAGAGACTGAGCT 60.680 60.000 0.00 0.00 0.00 4.09
133 134 1.806568 CACCTCCGAGAGACTGAGC 59.193 63.158 0.00 0.00 0.00 4.26
134 135 0.679640 AGCACCTCCGAGAGACTGAG 60.680 60.000 0.00 0.00 0.00 3.35
135 136 0.678366 GAGCACCTCCGAGAGACTGA 60.678 60.000 0.00 0.00 0.00 3.41
136 137 0.962855 TGAGCACCTCCGAGAGACTG 60.963 60.000 0.00 0.22 0.00 3.51
137 138 0.033601 ATGAGCACCTCCGAGAGACT 60.034 55.000 0.00 0.00 0.00 3.24
138 139 1.606668 CTATGAGCACCTCCGAGAGAC 59.393 57.143 0.00 0.00 0.00 3.36
139 140 1.477740 CCTATGAGCACCTCCGAGAGA 60.478 57.143 0.00 0.00 0.00 3.10
140 141 0.958091 CCTATGAGCACCTCCGAGAG 59.042 60.000 0.00 0.00 0.00 3.20
141 142 0.468214 CCCTATGAGCACCTCCGAGA 60.468 60.000 0.00 0.00 0.00 4.04
142 143 1.467678 CCCCTATGAGCACCTCCGAG 61.468 65.000 0.00 0.00 0.00 4.63
143 144 1.457643 CCCCTATGAGCACCTCCGA 60.458 63.158 0.00 0.00 0.00 4.55
144 145 0.469331 TACCCCTATGAGCACCTCCG 60.469 60.000 0.00 0.00 0.00 4.63
145 146 1.343069 CTACCCCTATGAGCACCTCC 58.657 60.000 0.00 0.00 0.00 4.30
146 147 1.343069 CCTACCCCTATGAGCACCTC 58.657 60.000 0.00 0.00 0.00 3.85
147 148 0.104934 CCCTACCCCTATGAGCACCT 60.105 60.000 0.00 0.00 0.00 4.00
148 149 0.400093 ACCCTACCCCTATGAGCACC 60.400 60.000 0.00 0.00 0.00 5.01
149 150 0.759346 CACCCTACCCCTATGAGCAC 59.241 60.000 0.00 0.00 0.00 4.40
150 151 0.341961 ACACCCTACCCCTATGAGCA 59.658 55.000 0.00 0.00 0.00 4.26
151 152 0.759346 CACACCCTACCCCTATGAGC 59.241 60.000 0.00 0.00 0.00 4.26
152 153 0.759346 GCACACCCTACCCCTATGAG 59.241 60.000 0.00 0.00 0.00 2.90
153 154 1.046472 CGCACACCCTACCCCTATGA 61.046 60.000 0.00 0.00 0.00 2.15
154 155 1.335132 ACGCACACCCTACCCCTATG 61.335 60.000 0.00 0.00 0.00 2.23
155 156 1.002533 ACGCACACCCTACCCCTAT 59.997 57.895 0.00 0.00 0.00 2.57
156 157 1.985662 CACGCACACCCTACCCCTA 60.986 63.158 0.00 0.00 0.00 3.53
157 158 3.319198 CACGCACACCCTACCCCT 61.319 66.667 0.00 0.00 0.00 4.79
158 159 3.633116 ACACGCACACCCTACCCC 61.633 66.667 0.00 0.00 0.00 4.95
159 160 2.358247 CACACGCACACCCTACCC 60.358 66.667 0.00 0.00 0.00 3.69
160 161 1.959226 CACACACGCACACCCTACC 60.959 63.158 0.00 0.00 0.00 3.18
161 162 2.604174 GCACACACGCACACCCTAC 61.604 63.158 0.00 0.00 0.00 3.18
162 163 2.280524 GCACACACGCACACCCTA 60.281 61.111 0.00 0.00 0.00 3.53
165 166 2.037913 TTAACGCACACACGCACACC 62.038 55.000 0.00 0.00 36.19 4.16
166 167 0.041663 ATTAACGCACACACGCACAC 60.042 50.000 0.00 0.00 36.19 3.82
167 168 1.457683 CTATTAACGCACACACGCACA 59.542 47.619 0.00 0.00 36.19 4.57
168 169 1.201877 CCTATTAACGCACACACGCAC 60.202 52.381 0.00 0.00 36.19 5.34
169 170 1.072391 CCTATTAACGCACACACGCA 58.928 50.000 0.00 0.00 36.19 5.24
170 171 0.372334 CCCTATTAACGCACACACGC 59.628 55.000 0.00 0.00 36.19 5.34
171 172 1.999048 TCCCTATTAACGCACACACG 58.001 50.000 0.00 0.00 39.50 4.49
172 173 3.527533 TCATCCCTATTAACGCACACAC 58.472 45.455 0.00 0.00 0.00 3.82
173 174 3.196901 ACTCATCCCTATTAACGCACACA 59.803 43.478 0.00 0.00 0.00 3.72
174 175 3.555956 CACTCATCCCTATTAACGCACAC 59.444 47.826 0.00 0.00 0.00 3.82
175 176 3.196901 ACACTCATCCCTATTAACGCACA 59.803 43.478 0.00 0.00 0.00 4.57
176 177 3.793559 ACACTCATCCCTATTAACGCAC 58.206 45.455 0.00 0.00 0.00 5.34
177 178 5.538118 CATACACTCATCCCTATTAACGCA 58.462 41.667 0.00 0.00 0.00 5.24
178 179 4.389077 GCATACACTCATCCCTATTAACGC 59.611 45.833 0.00 0.00 0.00 4.84
179 180 4.621460 CGCATACACTCATCCCTATTAACG 59.379 45.833 0.00 0.00 0.00 3.18
180 181 4.389077 GCGCATACACTCATCCCTATTAAC 59.611 45.833 0.30 0.00 0.00 2.01
181 182 4.566004 GCGCATACACTCATCCCTATTAA 58.434 43.478 0.30 0.00 0.00 1.40
182 183 3.366985 CGCGCATACACTCATCCCTATTA 60.367 47.826 8.75 0.00 0.00 0.98
183 184 2.610479 CGCGCATACACTCATCCCTATT 60.610 50.000 8.75 0.00 0.00 1.73
184 185 1.067565 CGCGCATACACTCATCCCTAT 60.068 52.381 8.75 0.00 0.00 2.57
185 186 0.313987 CGCGCATACACTCATCCCTA 59.686 55.000 8.75 0.00 0.00 3.53
186 187 1.068083 CGCGCATACACTCATCCCT 59.932 57.895 8.75 0.00 0.00 4.20
187 188 1.227263 ACGCGCATACACTCATCCC 60.227 57.895 5.73 0.00 0.00 3.85
188 189 0.806102 ACACGCGCATACACTCATCC 60.806 55.000 5.73 0.00 0.00 3.51
189 190 1.835121 TACACGCGCATACACTCATC 58.165 50.000 5.73 0.00 0.00 2.92
190 191 2.509052 ATACACGCGCATACACTCAT 57.491 45.000 5.73 0.00 0.00 2.90
191 192 3.003897 TCATATACACGCGCATACACTCA 59.996 43.478 5.73 0.00 0.00 3.41
192 193 3.561503 TCATATACACGCGCATACACTC 58.438 45.455 5.73 0.00 0.00 3.51
193 194 3.565516 CTCATATACACGCGCATACACT 58.434 45.455 5.73 0.00 0.00 3.55
194 195 2.090658 GCTCATATACACGCGCATACAC 59.909 50.000 5.73 0.00 0.00 2.90
195 196 2.324860 GCTCATATACACGCGCATACA 58.675 47.619 5.73 0.00 0.00 2.29
196 197 1.317611 CGCTCATATACACGCGCATAC 59.682 52.381 5.73 0.00 39.11 2.39
197 198 1.613270 CGCTCATATACACGCGCATA 58.387 50.000 5.73 1.53 39.11 3.14
198 199 2.434688 CGCTCATATACACGCGCAT 58.565 52.632 5.73 0.00 39.11 4.73
199 200 3.916439 CGCTCATATACACGCGCA 58.084 55.556 5.73 0.00 39.11 6.09
203 204 2.193447 ACACAAGCGCTCATATACACG 58.807 47.619 12.06 0.00 0.00 4.49
204 205 4.142902 ACAAACACAAGCGCTCATATACAC 60.143 41.667 12.06 0.00 0.00 2.90
205 206 4.000325 ACAAACACAAGCGCTCATATACA 59.000 39.130 12.06 0.00 0.00 2.29
206 207 4.600012 ACAAACACAAGCGCTCATATAC 57.400 40.909 12.06 0.00 0.00 1.47
207 208 5.290885 CAGTACAAACACAAGCGCTCATATA 59.709 40.000 12.06 0.00 0.00 0.86
208 209 4.093408 CAGTACAAACACAAGCGCTCATAT 59.907 41.667 12.06 0.00 0.00 1.78
209 210 3.431912 CAGTACAAACACAAGCGCTCATA 59.568 43.478 12.06 0.00 0.00 2.15
210 211 2.224079 CAGTACAAACACAAGCGCTCAT 59.776 45.455 12.06 0.00 0.00 2.90
211 212 1.597195 CAGTACAAACACAAGCGCTCA 59.403 47.619 12.06 0.00 0.00 4.26
212 213 1.864711 TCAGTACAAACACAAGCGCTC 59.135 47.619 12.06 0.00 0.00 5.03
213 214 1.948104 TCAGTACAAACACAAGCGCT 58.052 45.000 2.64 2.64 0.00 5.92
214 215 2.574322 CATCAGTACAAACACAAGCGC 58.426 47.619 0.00 0.00 0.00 5.92
215 216 2.224079 AGCATCAGTACAAACACAAGCG 59.776 45.455 0.00 0.00 0.00 4.68
216 217 3.250762 TGAGCATCAGTACAAACACAAGC 59.749 43.478 0.00 0.00 42.56 4.01
242 243 7.763071 GTCAGTAGTATGATTACCGGACTTTTT 59.237 37.037 9.46 0.00 0.00 1.94
243 244 7.263496 GTCAGTAGTATGATTACCGGACTTTT 58.737 38.462 9.46 0.00 0.00 2.27
244 245 6.459298 CGTCAGTAGTATGATTACCGGACTTT 60.459 42.308 9.46 0.00 0.00 2.66
245 246 5.008415 CGTCAGTAGTATGATTACCGGACTT 59.992 44.000 9.46 0.00 0.00 3.01
246 247 4.514441 CGTCAGTAGTATGATTACCGGACT 59.486 45.833 9.46 0.68 0.00 3.85
247 248 4.320057 CCGTCAGTAGTATGATTACCGGAC 60.320 50.000 9.46 0.00 37.32 4.79
248 249 3.817084 CCGTCAGTAGTATGATTACCGGA 59.183 47.826 9.46 0.00 37.32 5.14
249 250 3.611057 GCCGTCAGTAGTATGATTACCGG 60.611 52.174 0.00 0.00 37.86 5.28
250 251 3.252701 AGCCGTCAGTAGTATGATTACCG 59.747 47.826 0.00 0.00 0.00 4.02
257 258 1.749063 TGTGGAGCCGTCAGTAGTATG 59.251 52.381 0.00 0.00 0.00 2.39
282 288 3.764237 TCCCGTATAAATCCTTCAGGC 57.236 47.619 0.00 0.00 34.44 4.85
474 513 6.461509 CCAGGAAATATATGGCTGGTGTTTTC 60.462 42.308 0.00 0.00 0.00 2.29
493 532 3.646715 CCGCCCAAGACCCAGGAA 61.647 66.667 0.00 0.00 0.00 3.36
544 1811 3.703001 TCAACCCTCCAAGAATCAGTC 57.297 47.619 0.00 0.00 0.00 3.51
546 1813 4.639310 CAGAATCAACCCTCCAAGAATCAG 59.361 45.833 0.00 0.00 0.00 2.90
549 1816 3.879321 GCCAGAATCAACCCTCCAAGAAT 60.879 47.826 0.00 0.00 0.00 2.40
551 1818 1.004745 GCCAGAATCAACCCTCCAAGA 59.995 52.381 0.00 0.00 0.00 3.02
553 1820 0.322456 CGCCAGAATCAACCCTCCAA 60.322 55.000 0.00 0.00 0.00 3.53
554 1821 1.299648 CGCCAGAATCAACCCTCCA 59.700 57.895 0.00 0.00 0.00 3.86
556 1823 1.377202 TGCGCCAGAATCAACCCTC 60.377 57.895 4.18 0.00 0.00 4.30
560 1841 2.480555 CGGTGCGCCAGAATCAAC 59.519 61.111 18.18 0.00 34.09 3.18
561 1842 2.745884 CCGGTGCGCCAGAATCAA 60.746 61.111 18.18 0.00 34.09 2.57
580 1861 1.371183 CACCTTGCCTCTCCGTCAA 59.629 57.895 0.00 0.00 0.00 3.18
658 1939 4.033776 GTACCTGCCCTGCCTGCA 62.034 66.667 0.00 0.00 37.17 4.41
678 1959 1.812571 CAATCACGGAAGGAAAGGGTG 59.187 52.381 0.00 0.00 0.00 4.61
679 1960 1.886655 GCAATCACGGAAGGAAAGGGT 60.887 52.381 0.00 0.00 0.00 4.34
822 2108 6.072286 CCTGCAAAATCACAGTGTTAGAATCT 60.072 38.462 0.00 0.00 31.76 2.40
876 2176 3.685139 AGAGTTTCGGCAGAAAGATGA 57.315 42.857 12.50 0.00 45.92 2.92
877 2177 3.748048 TGAAGAGTTTCGGCAGAAAGATG 59.252 43.478 12.50 0.00 45.92 2.90
908 2208 1.462283 CAGCTCTGTGTTCACCAATCG 59.538 52.381 0.37 0.00 0.00 3.34
926 2226 2.996249 TAATTCTCCTCCTGCTGCAG 57.004 50.000 22.44 22.44 0.00 4.41
927 2227 3.939740 AATAATTCTCCTCCTGCTGCA 57.060 42.857 0.88 0.88 0.00 4.41
930 2233 9.559496 AATCTATCTAATAATTCTCCTCCTGCT 57.441 33.333 0.00 0.00 0.00 4.24
1032 2340 0.534203 GCGACCTCTTTTCACCACCA 60.534 55.000 0.00 0.00 0.00 4.17
1035 2343 1.301401 CCGCGACCTCTTTTCACCA 60.301 57.895 8.23 0.00 0.00 4.17
1136 2450 3.500343 TGGTCATCAGAGTCAGAGTCAA 58.500 45.455 8.03 0.00 0.00 3.18
1475 2795 1.228094 TCGGTTGGATGTTGCAGCA 60.228 52.632 5.46 5.46 0.00 4.41
1940 3262 2.192263 GATCCTGTTCCTCCTCCACTT 58.808 52.381 0.00 0.00 0.00 3.16
2017 3339 0.687757 ATCCGCAGCTCTCCCTTGTA 60.688 55.000 0.00 0.00 0.00 2.41
2502 5752 2.938354 GCATGAGCGCCCAATAGAT 58.062 52.632 2.29 0.00 0.00 1.98
2551 5817 4.475135 GCGCTTCCACCCTCCCTC 62.475 72.222 0.00 0.00 0.00 4.30
2553 5819 4.115199 ATGCGCTTCCACCCTCCC 62.115 66.667 9.73 0.00 0.00 4.30
2554 5820 2.825836 CATGCGCTTCCACCCTCC 60.826 66.667 9.73 0.00 0.00 4.30
2625 5891 6.763135 CCTTTGATATACTCTAGCAACAGCAA 59.237 38.462 0.00 0.00 0.00 3.91
2671 6121 1.664016 GCACCTCACGTTTCTTGCATG 60.664 52.381 4.52 0.00 0.00 4.06
2672 6122 0.593128 GCACCTCACGTTTCTTGCAT 59.407 50.000 4.52 0.00 0.00 3.96
2673 6123 0.463654 AGCACCTCACGTTTCTTGCA 60.464 50.000 10.60 0.00 32.24 4.08
2674 6124 0.663153 AAGCACCTCACGTTTCTTGC 59.337 50.000 0.00 0.00 0.00 4.01
2675 6125 1.670811 ACAAGCACCTCACGTTTCTTG 59.329 47.619 0.00 0.00 37.97 3.02
2676 6126 2.038387 ACAAGCACCTCACGTTTCTT 57.962 45.000 0.00 0.00 0.00 2.52
2677 6127 2.364324 TCTACAAGCACCTCACGTTTCT 59.636 45.455 0.00 0.00 0.00 2.52
2825 7634 8.037382 AGCCAACTGATTCATATTCATATTCG 57.963 34.615 0.00 0.00 0.00 3.34
2836 7651 9.461312 TTTATAGTGTTTAGCCAACTGATTCAT 57.539 29.630 0.00 0.00 36.21 2.57
2837 7652 8.856153 TTTATAGTGTTTAGCCAACTGATTCA 57.144 30.769 0.00 0.00 36.21 2.57
2838 7653 9.937175 GATTTATAGTGTTTAGCCAACTGATTC 57.063 33.333 0.00 0.00 36.21 2.52
2839 7654 8.903820 GGATTTATAGTGTTTAGCCAACTGATT 58.096 33.333 0.00 0.00 36.21 2.57
2840 7655 8.275040 AGGATTTATAGTGTTTAGCCAACTGAT 58.725 33.333 0.00 0.00 36.21 2.90
2841 7656 7.552687 CAGGATTTATAGTGTTTAGCCAACTGA 59.447 37.037 0.00 0.00 36.21 3.41
2842 7657 7.679638 GCAGGATTTATAGTGTTTAGCCAACTG 60.680 40.741 0.00 0.00 36.21 3.16
2843 7658 6.318900 GCAGGATTTATAGTGTTTAGCCAACT 59.681 38.462 0.00 0.00 36.21 3.16
2844 7659 6.459710 GGCAGGATTTATAGTGTTTAGCCAAC 60.460 42.308 0.00 0.00 37.23 3.77
2916 7731 4.571580 GCAGGAACTCTTGAGAAGATCATG 59.428 45.833 4.49 6.31 34.60 3.07
2917 7732 4.680172 CGCAGGAACTCTTGAGAAGATCAT 60.680 45.833 4.49 0.00 34.60 2.45
2918 7733 3.367806 CGCAGGAACTCTTGAGAAGATCA 60.368 47.826 4.49 0.00 34.60 2.92
2919 7734 3.119316 TCGCAGGAACTCTTGAGAAGATC 60.119 47.826 4.49 0.00 34.60 2.75
2961 7776 3.831911 CCTTTTCAACCTTGAGGCCATAA 59.168 43.478 5.01 0.00 38.61 1.90
2963 7778 2.250924 CCTTTTCAACCTTGAGGCCAT 58.749 47.619 5.01 0.00 38.61 4.40
2980 7795 2.352805 GCTGGGCTACTGCACCTT 59.647 61.111 6.08 0.00 43.18 3.50
3006 7821 2.359107 CACGCCATCAGCACACCT 60.359 61.111 0.00 0.00 44.04 4.00
3009 7824 4.639906 TGGCACGCCATCAGCACA 62.640 61.111 6.67 0.00 44.04 4.57
3024 7839 3.316573 GACTTCCCTGGGCTCGTGG 62.317 68.421 8.22 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.