Multiple sequence alignment - TraesCS4B01G348000

Loading Multiple Alignment...

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 TraesCS4B01G348000 chr4B 100.000 3292 0 0 1 3292 641520732 641524023 0.000000e+00 6080.0
1 TraesCS4B01G348000 chr4B 96.772 2571 74 8 726 3292 641541739 641544304 0.000000e+00 4279.0
2 TraesCS4B01G348000 chr4B 93.109 2409 123 22 888 3292 641685775 641688144 0.000000e+00 3489.0
3 TraesCS4B01G348000 chr4B 93.068 2409 124 22 888 3292 641777442 641779811 0.000000e+00 3483.0
4 TraesCS4B01G348000 chr4B 93.026 2409 125 22 888 3292 641646373 641648742 0.000000e+00 3478.0
5 TraesCS4B01G348000 chr4B 92.985 2409 124 24 888 3292 641568488 641570855 0.000000e+00 3470.0
6 TraesCS4B01G348000 chr4B 92.863 2410 128 23 888 3292 641609669 641612039 0.000000e+00 3458.0
7 TraesCS4B01G348000 chr4B 92.659 2343 129 26 953 3290 641482401 641484705 0.000000e+00 3334.0
8 TraesCS4B01G348000 chr4B 97.481 675 6 3 324 987 641481736 641482410 0.000000e+00 1142.0
9 TraesCS4B01G348000 chr4B 93.492 461 18 6 477 925 641540602 641541062 0.000000e+00 675.0
10 TraesCS4B01G348000 chr4B 92.857 168 10 2 324 491 641538675 641538840 3.280000e-60 243.0
11 TraesCS4B01G348000 chr4B 81.140 228 23 7 444 659 641567981 641568200 7.310000e-37 165.0
12 TraesCS4B01G348000 chr4B 81.140 228 23 7 444 659 641609162 641609381 7.310000e-37 165.0
13 TraesCS4B01G348000 chr4B 81.140 228 23 7 444 659 641645866 641646085 7.310000e-37 165.0
14 TraesCS4B01G348000 chr4B 81.140 228 23 7 444 659 641685268 641685487 7.310000e-37 165.0
15 TraesCS4B01G348000 chr5A 92.292 1998 127 13 953 2937 679778252 679780235 0.000000e+00 2811.0
16 TraesCS4B01G348000 chr5A 91.002 589 24 15 415 987 679777686 679778261 0.000000e+00 767.0
17 TraesCS4B01G348000 chrUn 96.731 1346 35 4 975 2320 410175031 410173695 0.000000e+00 2233.0
18 TraesCS4B01G348000 chrUn 81.140 228 23 7 444 659 421756601 421756820 7.310000e-37 165.0
19 TraesCS4B01G348000 chrUn 81.169 154 20 7 172 321 50966651 50966799 7.460000e-22 115.0
20 TraesCS4B01G348000 chr4D 90.595 1244 66 30 324 1527 499106748 499107980 0.000000e+00 1602.0
21 TraesCS4B01G348000 chr4D 86.677 1246 83 43 319 1527 499166917 499168116 0.000000e+00 1304.0
22 TraesCS4B01G348000 chr4D 86.597 1246 84 43 319 1527 499120153 499121352 0.000000e+00 1299.0
23 TraesCS4B01G348000 chr4D 94.436 629 22 8 768 1393 499136509 499137127 0.000000e+00 955.0
24 TraesCS4B01G348000 chr4D 94.436 629 22 8 768 1393 499149124 499149742 0.000000e+00 955.0
25 TraesCS4B01G348000 chr4D 88.089 403 39 4 2898 3292 499169573 499169974 1.380000e-128 470.0
26 TraesCS4B01G348000 chr3B 84.772 197 28 2 124 320 759489509 759489703 2.590000e-46 196.0
27 TraesCS4B01G348000 chr5B 91.736 121 9 1 201 321 156304682 156304563 2.030000e-37 167.0
28 TraesCS4B01G348000 chr2D 91.071 112 10 0 209 320 229582037 229582148 5.690000e-33 152.0
29 TraesCS4B01G348000 chr2D 90.265 113 11 0 209 321 123925880 123925768 7.360000e-32 148.0
30 TraesCS4B01G348000 chr4A 79.058 191 28 11 131 316 627619926 627620109 1.600000e-23 121.0
31 TraesCS4B01G348000 chr4A 80.315 127 20 5 197 321 613745166 613745043 1.260000e-14 91.6
32 TraesCS4B01G348000 chr4A 92.000 50 4 0 344 393 709686621 709686670 1.640000e-08 71.3
33 TraesCS4B01G348000 chr2B 82.906 117 18 2 210 325 122590216 122590101 1.620000e-18 104.0
34 TraesCS4B01G348000 chr7D 79.845 129 24 2 188 316 2858308 2858434 3.500000e-15 93.5


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 TraesCS4B01G348000 chr4B 641520732 641524023 3291 False 6080.000000 6080 100.000000 1 3292 1 chr4B.!!$F1 3291
1 TraesCS4B01G348000 chr4B 641777442 641779811 2369 False 3483.000000 3483 93.068000 888 3292 1 chr4B.!!$F2 2404
2 TraesCS4B01G348000 chr4B 641481736 641484705 2969 False 2238.000000 3334 95.070000 324 3290 2 chr4B.!!$F3 2966
3 TraesCS4B01G348000 chr4B 641685268 641688144 2876 False 1827.000000 3489 87.124500 444 3292 2 chr4B.!!$F8 2848
4 TraesCS4B01G348000 chr4B 641645866 641648742 2876 False 1821.500000 3478 87.083000 444 3292 2 chr4B.!!$F7 2848
5 TraesCS4B01G348000 chr4B 641567981 641570855 2874 False 1817.500000 3470 87.062500 444 3292 2 chr4B.!!$F5 2848
6 TraesCS4B01G348000 chr4B 641609162 641612039 2877 False 1811.500000 3458 87.001500 444 3292 2 chr4B.!!$F6 2848
7 TraesCS4B01G348000 chr4B 641538675 641544304 5629 False 1732.333333 4279 94.373667 324 3292 3 chr4B.!!$F4 2968
8 TraesCS4B01G348000 chr5A 679777686 679780235 2549 False 1789.000000 2811 91.647000 415 2937 2 chr5A.!!$F1 2522
9 TraesCS4B01G348000 chrUn 410173695 410175031 1336 True 2233.000000 2233 96.731000 975 2320 1 chrUn.!!$R1 1345
10 TraesCS4B01G348000 chr4D 499106748 499107980 1232 False 1602.000000 1602 90.595000 324 1527 1 chr4D.!!$F1 1203
11 TraesCS4B01G348000 chr4D 499120153 499121352 1199 False 1299.000000 1299 86.597000 319 1527 1 chr4D.!!$F2 1208
12 TraesCS4B01G348000 chr4D 499136509 499137127 618 False 955.000000 955 94.436000 768 1393 1 chr4D.!!$F3 625
13 TraesCS4B01G348000 chr4D 499149124 499149742 618 False 955.000000 955 94.436000 768 1393 1 chr4D.!!$F4 625
14 TraesCS4B01G348000 chr4D 499166917 499169974 3057 False 887.000000 1304 87.383000 319 3292 2 chr4D.!!$F5 2973

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
203 204 0.032815 GGGATAAGAGAGCACGCCTC 59.967 60.0 0.0 0.0 41.07 4.70 F
297 298 0.037697 TGTGGTGTCTCGTATGGTGC 60.038 55.0 0.0 0.0 0.00 5.01 F
300 301 0.249398 GGTGTCTCGTATGGTGCCTT 59.751 55.0 0.0 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 4918 0.250038 GGTCTCTGCTGCTGTTGTCA 60.250 55.000 0.0 0.0 0.0 3.58 R
2289 5111 0.033503 TCCACGCCATAGACCTCTCA 60.034 55.000 0.0 0.0 0.0 3.27 R
2356 5178 1.271543 TGGTTGAAGTCATGCTGGGAG 60.272 52.381 0.0 0.0 0.0 4.30 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
46 47 2.612285 ACTCCAGAGTCCATGTCTCA 57.388 50.000 14.61 0.00 36.92 3.27
47 48 2.455557 ACTCCAGAGTCCATGTCTCAG 58.544 52.381 14.61 8.50 36.92 3.35
48 49 2.042297 ACTCCAGAGTCCATGTCTCAGA 59.958 50.000 14.61 10.63 36.92 3.27
49 50 3.298619 CTCCAGAGTCCATGTCTCAGAT 58.701 50.000 14.61 0.00 34.73 2.90
50 51 3.705579 CTCCAGAGTCCATGTCTCAGATT 59.294 47.826 14.61 0.00 34.73 2.40
51 52 4.099633 TCCAGAGTCCATGTCTCAGATTT 58.900 43.478 14.61 0.00 34.73 2.17
52 53 4.161189 TCCAGAGTCCATGTCTCAGATTTC 59.839 45.833 14.61 0.00 34.73 2.17
53 54 4.440880 CAGAGTCCATGTCTCAGATTTCC 58.559 47.826 14.61 0.00 34.73 3.13
54 55 4.161942 CAGAGTCCATGTCTCAGATTTCCT 59.838 45.833 14.61 0.00 34.73 3.36
55 56 4.782156 AGAGTCCATGTCTCAGATTTCCTT 59.218 41.667 14.61 0.00 34.73 3.36
56 57 5.250313 AGAGTCCATGTCTCAGATTTCCTTT 59.750 40.000 14.61 0.00 34.73 3.11
57 58 5.885465 AGTCCATGTCTCAGATTTCCTTTT 58.115 37.500 0.00 0.00 0.00 2.27
58 59 6.310149 AGTCCATGTCTCAGATTTCCTTTTT 58.690 36.000 0.00 0.00 0.00 1.94
81 82 7.480760 TTTTTCCTTATTCAAGGGAATGGAG 57.519 36.000 3.68 0.00 46.86 3.86
82 83 6.799827 TTTTCCTTATTCAAGGGAATGGAGA 58.200 36.000 3.68 0.00 46.86 3.71
83 84 6.891908 TTTTCCTTATTCAAGGGAATGGAGAG 59.108 38.462 3.68 0.00 46.86 3.20
84 85 5.379706 CCTTATTCAAGGGAATGGAGAGT 57.620 43.478 0.41 0.00 46.71 3.24
85 86 5.372373 CCTTATTCAAGGGAATGGAGAGTC 58.628 45.833 0.41 0.00 46.71 3.36
86 87 3.941704 ATTCAAGGGAATGGAGAGTCC 57.058 47.619 0.00 0.00 42.10 3.85
87 88 2.649742 TCAAGGGAATGGAGAGTCCT 57.350 50.000 0.00 0.00 36.52 3.85
88 89 3.776731 TCAAGGGAATGGAGAGTCCTA 57.223 47.619 0.00 0.00 36.52 2.94
89 90 3.647636 TCAAGGGAATGGAGAGTCCTAG 58.352 50.000 0.00 0.00 36.52 3.02
90 91 3.012959 TCAAGGGAATGGAGAGTCCTAGT 59.987 47.826 0.00 0.00 36.52 2.57
91 92 3.039252 AGGGAATGGAGAGTCCTAGTG 57.961 52.381 0.00 0.00 36.52 2.74
92 93 2.587777 AGGGAATGGAGAGTCCTAGTGA 59.412 50.000 0.00 0.00 36.52 3.41
93 94 3.012959 AGGGAATGGAGAGTCCTAGTGAA 59.987 47.826 0.00 0.00 36.52 3.18
94 95 3.970640 GGGAATGGAGAGTCCTAGTGAAT 59.029 47.826 0.00 0.00 36.52 2.57
95 96 4.039852 GGGAATGGAGAGTCCTAGTGAATC 59.960 50.000 0.00 1.79 36.52 2.52
96 97 4.651503 GGAATGGAGAGTCCTAGTGAATCA 59.348 45.833 10.08 0.00 40.53 2.57
97 98 5.452636 GGAATGGAGAGTCCTAGTGAATCAC 60.453 48.000 5.02 5.02 40.53 3.06
98 99 4.047627 TGGAGAGTCCTAGTGAATCACA 57.952 45.455 16.38 1.00 40.53 3.58
99 100 3.764434 TGGAGAGTCCTAGTGAATCACAC 59.236 47.826 16.38 4.85 40.53 3.82
100 101 4.509302 TGGAGAGTCCTAGTGAATCACACT 60.509 45.833 16.38 9.82 46.83 3.55
101 102 5.987303 TGGAGAGTCCTAGTGAATCACACTT 60.987 44.000 16.38 0.00 46.31 3.16
102 103 7.971569 TGGAGAGTCCTAGTGAATCACACTTG 61.972 46.154 16.38 7.37 46.31 3.16
109 110 1.613437 GTGAATCACACTTGGGTTGGG 59.387 52.381 8.74 0.00 45.13 4.12
110 111 1.496857 TGAATCACACTTGGGTTGGGA 59.503 47.619 0.00 0.00 0.00 4.37
111 112 2.109834 TGAATCACACTTGGGTTGGGAT 59.890 45.455 0.00 0.00 0.00 3.85
112 113 3.332187 TGAATCACACTTGGGTTGGGATA 59.668 43.478 0.00 0.00 0.00 2.59
113 114 3.652057 ATCACACTTGGGTTGGGATAG 57.348 47.619 0.00 0.00 0.00 2.08
114 115 1.633432 TCACACTTGGGTTGGGATAGG 59.367 52.381 0.00 0.00 0.00 2.57
115 116 1.633432 CACACTTGGGTTGGGATAGGA 59.367 52.381 0.00 0.00 0.00 2.94
116 117 1.916181 ACACTTGGGTTGGGATAGGAG 59.084 52.381 0.00 0.00 0.00 3.69
117 118 2.196595 CACTTGGGTTGGGATAGGAGA 58.803 52.381 0.00 0.00 0.00 3.71
118 119 2.171448 CACTTGGGTTGGGATAGGAGAG 59.829 54.545 0.00 0.00 0.00 3.20
119 120 1.141858 CTTGGGTTGGGATAGGAGAGC 59.858 57.143 0.00 0.00 0.00 4.09
120 121 0.044092 TGGGTTGGGATAGGAGAGCA 59.956 55.000 0.00 0.00 0.00 4.26
121 122 0.761802 GGGTTGGGATAGGAGAGCAG 59.238 60.000 0.00 0.00 0.00 4.24
122 123 0.761802 GGTTGGGATAGGAGAGCAGG 59.238 60.000 0.00 0.00 0.00 4.85
123 124 0.107643 GTTGGGATAGGAGAGCAGGC 59.892 60.000 0.00 0.00 0.00 4.85
124 125 1.056700 TTGGGATAGGAGAGCAGGCC 61.057 60.000 0.00 0.00 0.00 5.19
125 126 1.152139 GGGATAGGAGAGCAGGCCT 60.152 63.158 0.00 0.00 38.31 5.19
126 127 1.191489 GGGATAGGAGAGCAGGCCTC 61.191 65.000 0.00 0.00 41.07 4.70
127 128 0.470833 GGATAGGAGAGCAGGCCTCA 60.471 60.000 0.00 0.00 43.31 3.86
128 129 0.678950 GATAGGAGAGCAGGCCTCAC 59.321 60.000 0.00 0.00 43.31 3.51
129 130 1.112315 ATAGGAGAGCAGGCCTCACG 61.112 60.000 0.00 0.00 43.31 4.35
130 131 2.500815 TAGGAGAGCAGGCCTCACGT 62.501 60.000 0.00 0.00 43.31 4.49
131 132 2.659610 GAGAGCAGGCCTCACGTT 59.340 61.111 0.00 0.00 43.31 3.99
132 133 1.004440 GAGAGCAGGCCTCACGTTT 60.004 57.895 0.00 0.00 43.31 3.60
133 134 0.246635 GAGAGCAGGCCTCACGTTTA 59.753 55.000 0.00 0.00 43.31 2.01
134 135 0.905357 AGAGCAGGCCTCACGTTTAT 59.095 50.000 0.00 0.00 43.31 1.40
135 136 1.279271 AGAGCAGGCCTCACGTTTATT 59.721 47.619 0.00 0.00 43.31 1.40
136 137 2.500098 AGAGCAGGCCTCACGTTTATTA 59.500 45.455 0.00 0.00 43.31 0.98
137 138 3.134804 AGAGCAGGCCTCACGTTTATTAT 59.865 43.478 0.00 0.00 43.31 1.28
138 139 3.877508 GAGCAGGCCTCACGTTTATTATT 59.122 43.478 0.00 0.00 40.45 1.40
139 140 3.877508 AGCAGGCCTCACGTTTATTATTC 59.122 43.478 0.00 0.00 0.00 1.75
140 141 3.625764 GCAGGCCTCACGTTTATTATTCA 59.374 43.478 0.00 0.00 0.00 2.57
141 142 4.095782 GCAGGCCTCACGTTTATTATTCAA 59.904 41.667 0.00 0.00 0.00 2.69
142 143 5.730568 GCAGGCCTCACGTTTATTATTCAAG 60.731 44.000 0.00 0.00 0.00 3.02
143 144 4.881850 AGGCCTCACGTTTATTATTCAAGG 59.118 41.667 0.00 0.00 0.00 3.61
144 145 4.036380 GGCCTCACGTTTATTATTCAAGGG 59.964 45.833 0.00 0.00 0.00 3.95
145 146 4.879545 GCCTCACGTTTATTATTCAAGGGA 59.120 41.667 0.00 0.00 0.00 4.20
146 147 5.007724 GCCTCACGTTTATTATTCAAGGGAG 59.992 44.000 0.00 0.00 0.00 4.30
147 148 6.346096 CCTCACGTTTATTATTCAAGGGAGA 58.654 40.000 0.00 0.00 0.00 3.71
148 149 6.480320 CCTCACGTTTATTATTCAAGGGAGAG 59.520 42.308 0.00 0.00 0.00 3.20
149 150 7.177832 TCACGTTTATTATTCAAGGGAGAGA 57.822 36.000 0.00 0.00 0.00 3.10
150 151 7.265673 TCACGTTTATTATTCAAGGGAGAGAG 58.734 38.462 0.00 0.00 0.00 3.20
151 152 7.123697 TCACGTTTATTATTCAAGGGAGAGAGA 59.876 37.037 0.00 0.00 0.00 3.10
152 153 7.436673 CACGTTTATTATTCAAGGGAGAGAGAG 59.563 40.741 0.00 0.00 0.00 3.20
153 154 7.342284 ACGTTTATTATTCAAGGGAGAGAGAGA 59.658 37.037 0.00 0.00 0.00 3.10
154 155 7.865385 CGTTTATTATTCAAGGGAGAGAGAGAG 59.135 40.741 0.00 0.00 0.00 3.20
155 156 8.919145 GTTTATTATTCAAGGGAGAGAGAGAGA 58.081 37.037 0.00 0.00 0.00 3.10
156 157 8.704849 TTATTATTCAAGGGAGAGAGAGAGAG 57.295 38.462 0.00 0.00 0.00 3.20
157 158 4.608170 ATTCAAGGGAGAGAGAGAGAGT 57.392 45.455 0.00 0.00 0.00 3.24
158 159 3.644966 TCAAGGGAGAGAGAGAGAGTC 57.355 52.381 0.00 0.00 0.00 3.36
159 160 2.241176 TCAAGGGAGAGAGAGAGAGTCC 59.759 54.545 0.00 0.00 0.00 3.85
160 161 2.242196 CAAGGGAGAGAGAGAGAGTCCT 59.758 54.545 0.00 0.00 0.00 3.85
161 162 3.431411 AGGGAGAGAGAGAGAGTCCTA 57.569 52.381 0.00 0.00 0.00 2.94
162 163 3.743132 AGGGAGAGAGAGAGAGTCCTAA 58.257 50.000 0.00 0.00 0.00 2.69
163 164 4.315993 AGGGAGAGAGAGAGAGTCCTAAT 58.684 47.826 0.00 0.00 0.00 1.73
164 165 4.104738 AGGGAGAGAGAGAGAGTCCTAATG 59.895 50.000 0.00 0.00 0.00 1.90
165 166 4.398319 GGAGAGAGAGAGAGTCCTAATGG 58.602 52.174 0.00 0.00 0.00 3.16
166 167 4.104102 GGAGAGAGAGAGAGTCCTAATGGA 59.896 50.000 0.00 0.00 40.69 3.41
167 168 5.398581 GGAGAGAGAGAGAGTCCTAATGGAA 60.399 48.000 0.00 0.00 45.18 3.53
168 169 6.086011 AGAGAGAGAGAGTCCTAATGGAAA 57.914 41.667 0.00 0.00 45.18 3.13
169 170 6.498538 AGAGAGAGAGAGTCCTAATGGAAAA 58.501 40.000 0.00 0.00 45.18 2.29
170 171 6.379988 AGAGAGAGAGAGTCCTAATGGAAAAC 59.620 42.308 0.00 0.00 45.18 2.43
171 172 5.126384 AGAGAGAGAGTCCTAATGGAAAACG 59.874 44.000 0.00 0.00 45.18 3.60
172 173 5.017490 AGAGAGAGTCCTAATGGAAAACGA 58.983 41.667 0.00 0.00 45.18 3.85
173 174 5.074584 AGAGAGTCCTAATGGAAAACGAC 57.925 43.478 0.00 0.00 45.18 4.34
174 175 4.773149 AGAGAGTCCTAATGGAAAACGACT 59.227 41.667 0.00 0.00 45.18 4.18
175 176 5.074584 AGAGTCCTAATGGAAAACGACTC 57.925 43.478 6.87 6.87 45.18 3.36
176 177 5.074584 GAGTCCTAATGGAAAACGACTCT 57.925 43.478 7.57 0.00 45.18 3.24
177 178 5.480205 GAGTCCTAATGGAAAACGACTCTT 58.520 41.667 7.57 0.00 45.18 2.85
178 179 5.238583 AGTCCTAATGGAAAACGACTCTTG 58.761 41.667 0.00 0.00 45.18 3.02
179 180 4.995487 GTCCTAATGGAAAACGACTCTTGT 59.005 41.667 0.00 0.00 45.18 3.16
180 181 6.014840 AGTCCTAATGGAAAACGACTCTTGTA 60.015 38.462 0.00 0.00 45.18 2.41
181 182 6.310711 GTCCTAATGGAAAACGACTCTTGTAG 59.689 42.308 0.00 0.00 45.18 2.74
182 183 6.209986 TCCTAATGGAAAACGACTCTTGTAGA 59.790 38.462 0.00 0.00 39.87 2.59
183 184 7.042335 CCTAATGGAAAACGACTCTTGTAGAT 58.958 38.462 0.00 0.00 34.57 1.98
184 185 6.727824 AATGGAAAACGACTCTTGTAGATG 57.272 37.500 0.00 0.00 0.00 2.90
185 186 4.566004 TGGAAAACGACTCTTGTAGATGG 58.434 43.478 0.00 0.00 0.00 3.51
186 187 3.933332 GGAAAACGACTCTTGTAGATGGG 59.067 47.826 0.00 0.00 0.00 4.00
187 188 4.322499 GGAAAACGACTCTTGTAGATGGGA 60.322 45.833 0.00 0.00 0.00 4.37
188 189 5.420409 GAAAACGACTCTTGTAGATGGGAT 58.580 41.667 0.00 0.00 0.00 3.85
189 190 6.406624 GGAAAACGACTCTTGTAGATGGGATA 60.407 42.308 0.00 0.00 0.00 2.59
190 191 6.540438 AAACGACTCTTGTAGATGGGATAA 57.460 37.500 0.00 0.00 0.00 1.75
191 192 5.776173 ACGACTCTTGTAGATGGGATAAG 57.224 43.478 0.00 0.00 0.00 1.73
192 193 5.446860 ACGACTCTTGTAGATGGGATAAGA 58.553 41.667 0.00 0.00 0.00 2.10
193 194 5.533154 ACGACTCTTGTAGATGGGATAAGAG 59.467 44.000 9.92 9.92 46.00 2.85
194 195 5.765677 CGACTCTTGTAGATGGGATAAGAGA 59.234 44.000 16.49 0.00 44.32 3.10
195 196 6.072728 CGACTCTTGTAGATGGGATAAGAGAG 60.073 46.154 16.49 5.00 44.32 3.20
196 197 5.538433 ACTCTTGTAGATGGGATAAGAGAGC 59.462 44.000 16.49 0.00 44.32 4.09
197 198 5.458595 TCTTGTAGATGGGATAAGAGAGCA 58.541 41.667 0.00 0.00 0.00 4.26
198 199 5.303078 TCTTGTAGATGGGATAAGAGAGCAC 59.697 44.000 0.00 0.00 0.00 4.40
199 200 3.570125 TGTAGATGGGATAAGAGAGCACG 59.430 47.826 0.00 0.00 0.00 5.34
200 201 1.342819 AGATGGGATAAGAGAGCACGC 59.657 52.381 0.00 0.00 0.00 5.34
201 202 0.394565 ATGGGATAAGAGAGCACGCC 59.605 55.000 0.00 0.00 0.00 5.68
202 203 0.687757 TGGGATAAGAGAGCACGCCT 60.688 55.000 0.00 0.00 0.00 5.52
203 204 0.032815 GGGATAAGAGAGCACGCCTC 59.967 60.000 0.00 0.00 41.07 4.70
204 205 0.747255 GGATAAGAGAGCACGCCTCA 59.253 55.000 6.48 0.00 43.31 3.86
205 206 1.537135 GGATAAGAGAGCACGCCTCAC 60.537 57.143 6.48 0.58 43.31 3.51
215 216 3.093278 CGCCTCACGCTTTCATCC 58.907 61.111 0.00 0.00 34.21 3.51
216 217 1.741401 CGCCTCACGCTTTCATCCA 60.741 57.895 0.00 0.00 34.21 3.41
217 218 1.298157 CGCCTCACGCTTTCATCCAA 61.298 55.000 0.00 0.00 34.21 3.53
218 219 1.098050 GCCTCACGCTTTCATCCAAT 58.902 50.000 0.00 0.00 0.00 3.16
219 220 1.202222 GCCTCACGCTTTCATCCAATG 60.202 52.381 0.00 0.00 0.00 2.82
220 221 1.402968 CCTCACGCTTTCATCCAATGG 59.597 52.381 0.00 0.00 0.00 3.16
221 222 0.810648 TCACGCTTTCATCCAATGGC 59.189 50.000 0.00 0.00 0.00 4.40
222 223 0.813184 CACGCTTTCATCCAATGGCT 59.187 50.000 0.00 0.00 0.00 4.75
223 224 2.016318 CACGCTTTCATCCAATGGCTA 58.984 47.619 0.00 0.00 0.00 3.93
224 225 2.017049 ACGCTTTCATCCAATGGCTAC 58.983 47.619 0.00 0.00 0.00 3.58
225 226 2.016318 CGCTTTCATCCAATGGCTACA 58.984 47.619 0.00 0.00 0.00 2.74
226 227 2.423185 CGCTTTCATCCAATGGCTACAA 59.577 45.455 0.00 0.00 0.00 2.41
227 228 3.119531 CGCTTTCATCCAATGGCTACAAA 60.120 43.478 0.00 0.00 0.00 2.83
228 229 4.440525 CGCTTTCATCCAATGGCTACAAAT 60.441 41.667 0.00 0.00 0.00 2.32
229 230 5.221028 CGCTTTCATCCAATGGCTACAAATA 60.221 40.000 0.00 0.00 0.00 1.40
230 231 5.979517 GCTTTCATCCAATGGCTACAAATAC 59.020 40.000 0.00 0.00 0.00 1.89
231 232 6.405731 GCTTTCATCCAATGGCTACAAATACA 60.406 38.462 0.00 0.00 0.00 2.29
232 233 7.658525 TTTCATCCAATGGCTACAAATACAT 57.341 32.000 0.00 0.00 0.00 2.29
233 234 7.658525 TTCATCCAATGGCTACAAATACATT 57.341 32.000 0.00 0.00 34.13 2.71
234 235 8.759481 TTCATCCAATGGCTACAAATACATTA 57.241 30.769 0.00 0.00 32.71 1.90
235 236 8.938801 TCATCCAATGGCTACAAATACATTAT 57.061 30.769 0.00 0.00 32.71 1.28
264 265 9.855021 ATTAAATGGACGGTCAATTTTCTTTAG 57.145 29.630 24.36 0.00 0.00 1.85
265 266 6.894339 AATGGACGGTCAATTTTCTTTAGT 57.106 33.333 10.76 0.00 0.00 2.24
266 267 6.894339 ATGGACGGTCAATTTTCTTTAGTT 57.106 33.333 10.76 0.00 0.00 2.24
267 268 6.702716 TGGACGGTCAATTTTCTTTAGTTT 57.297 33.333 10.76 0.00 0.00 2.66
268 269 6.731164 TGGACGGTCAATTTTCTTTAGTTTC 58.269 36.000 10.76 0.00 0.00 2.78
269 270 6.319152 TGGACGGTCAATTTTCTTTAGTTTCA 59.681 34.615 10.76 0.00 0.00 2.69
270 271 6.635641 GGACGGTCAATTTTCTTTAGTTTCAC 59.364 38.462 10.76 0.00 0.00 3.18
271 272 6.196571 ACGGTCAATTTTCTTTAGTTTCACG 58.803 36.000 0.00 0.00 0.00 4.35
272 273 5.623673 CGGTCAATTTTCTTTAGTTTCACGG 59.376 40.000 0.00 0.00 0.00 4.94
273 274 6.500910 GGTCAATTTTCTTTAGTTTCACGGT 58.499 36.000 0.00 0.00 0.00 4.83
274 275 6.976349 GGTCAATTTTCTTTAGTTTCACGGTT 59.024 34.615 0.00 0.00 0.00 4.44
275 276 7.490079 GGTCAATTTTCTTTAGTTTCACGGTTT 59.510 33.333 0.00 0.00 0.00 3.27
276 277 9.505995 GTCAATTTTCTTTAGTTTCACGGTTTA 57.494 29.630 0.00 0.00 0.00 2.01
281 282 8.844441 TTTCTTTAGTTTCACGGTTTAATGTG 57.156 30.769 0.00 0.00 37.44 3.21
282 283 6.961576 TCTTTAGTTTCACGGTTTAATGTGG 58.038 36.000 0.00 0.00 36.74 4.17
283 284 6.543100 TCTTTAGTTTCACGGTTTAATGTGGT 59.457 34.615 0.00 0.00 36.74 4.16
284 285 4.561735 AGTTTCACGGTTTAATGTGGTG 57.438 40.909 0.00 0.00 36.74 4.17
285 286 3.949113 AGTTTCACGGTTTAATGTGGTGT 59.051 39.130 0.00 0.00 36.74 4.16
286 287 4.035909 AGTTTCACGGTTTAATGTGGTGTC 59.964 41.667 0.00 0.00 36.74 3.67
287 288 3.478857 TCACGGTTTAATGTGGTGTCT 57.521 42.857 0.00 0.00 36.74 3.41
288 289 3.395639 TCACGGTTTAATGTGGTGTCTC 58.604 45.455 0.00 0.00 36.74 3.36
289 290 2.156891 CACGGTTTAATGTGGTGTCTCG 59.843 50.000 0.00 0.00 32.47 4.04
290 291 2.224113 ACGGTTTAATGTGGTGTCTCGT 60.224 45.455 0.00 0.00 0.00 4.18
291 292 3.005684 ACGGTTTAATGTGGTGTCTCGTA 59.994 43.478 0.00 0.00 0.00 3.43
292 293 4.178540 CGGTTTAATGTGGTGTCTCGTAT 58.821 43.478 0.00 0.00 0.00 3.06
293 294 4.032445 CGGTTTAATGTGGTGTCTCGTATG 59.968 45.833 0.00 0.00 0.00 2.39
294 295 4.331717 GGTTTAATGTGGTGTCTCGTATGG 59.668 45.833 0.00 0.00 0.00 2.74
295 296 4.811969 TTAATGTGGTGTCTCGTATGGT 57.188 40.909 0.00 0.00 0.00 3.55
296 297 2.672961 ATGTGGTGTCTCGTATGGTG 57.327 50.000 0.00 0.00 0.00 4.17
297 298 0.037697 TGTGGTGTCTCGTATGGTGC 60.038 55.000 0.00 0.00 0.00 5.01
298 299 0.739813 GTGGTGTCTCGTATGGTGCC 60.740 60.000 0.00 0.00 0.00 5.01
299 300 0.902984 TGGTGTCTCGTATGGTGCCT 60.903 55.000 0.00 0.00 0.00 4.75
300 301 0.249398 GGTGTCTCGTATGGTGCCTT 59.751 55.000 0.00 0.00 0.00 4.35
301 302 1.641577 GTGTCTCGTATGGTGCCTTC 58.358 55.000 0.00 0.00 0.00 3.46
302 303 1.067142 GTGTCTCGTATGGTGCCTTCA 60.067 52.381 0.00 0.00 0.00 3.02
303 304 1.621317 TGTCTCGTATGGTGCCTTCAA 59.379 47.619 0.00 0.00 0.00 2.69
304 305 2.236146 TGTCTCGTATGGTGCCTTCAAT 59.764 45.455 0.00 0.00 0.00 2.57
305 306 3.270877 GTCTCGTATGGTGCCTTCAATT 58.729 45.455 0.00 0.00 0.00 2.32
306 307 4.081365 TGTCTCGTATGGTGCCTTCAATTA 60.081 41.667 0.00 0.00 0.00 1.40
307 308 4.508124 GTCTCGTATGGTGCCTTCAATTAG 59.492 45.833 0.00 0.00 0.00 1.73
308 309 4.161565 TCTCGTATGGTGCCTTCAATTAGT 59.838 41.667 0.00 0.00 0.00 2.24
309 310 5.361571 TCTCGTATGGTGCCTTCAATTAGTA 59.638 40.000 0.00 0.00 0.00 1.82
310 311 5.979993 TCGTATGGTGCCTTCAATTAGTAA 58.020 37.500 0.00 0.00 0.00 2.24
311 312 6.408035 TCGTATGGTGCCTTCAATTAGTAAA 58.592 36.000 0.00 0.00 0.00 2.01
312 313 7.051623 TCGTATGGTGCCTTCAATTAGTAAAT 58.948 34.615 0.00 0.00 0.00 1.40
313 314 8.205512 TCGTATGGTGCCTTCAATTAGTAAATA 58.794 33.333 0.00 0.00 0.00 1.40
314 315 8.999431 CGTATGGTGCCTTCAATTAGTAAATAT 58.001 33.333 0.00 0.00 0.00 1.28
729 2567 3.342370 TTGGCACACGCGCAAAACA 62.342 52.632 5.73 0.00 39.29 2.83
1134 3927 3.386237 GAGGAGCTGAGCCACGGT 61.386 66.667 0.00 0.00 0.00 4.83
1859 4681 3.031013 TGACTTCTCCGCCATTGATCTA 58.969 45.455 0.00 0.00 0.00 1.98
2094 4916 0.979709 CTGGATCTGGGCTGACTCCA 60.980 60.000 0.00 0.00 34.88 3.86
2096 4918 0.980231 GGATCTGGGCTGACTCCACT 60.980 60.000 0.00 0.00 0.00 4.00
2101 4923 1.053835 TGGGCTGACTCCACTGACAA 61.054 55.000 0.00 0.00 0.00 3.18
2289 5111 1.342174 TGGAAGAAGCCGTACTTTCGT 59.658 47.619 0.00 0.00 39.29 3.85
2356 5178 3.652292 GCGAGAAGCCTCTTACCTC 57.348 57.895 0.00 0.00 40.81 3.85
2434 5256 0.460311 AAATACGAGGAGACGCAGGG 59.540 55.000 0.00 0.00 36.70 4.45
2555 5377 5.920840 CACTGAATTCAACTCAGAGTACGAA 59.079 40.000 9.88 14.69 42.51 3.85
2791 5613 0.662619 TTTGAAGCCACACAAGAGCG 59.337 50.000 0.00 0.00 0.00 5.03
2844 5666 8.846211 GTTAGCAGTATTAAATAAAGCCATCCA 58.154 33.333 0.00 0.00 0.00 3.41
2902 5724 9.093970 TGATTCGATGGTGTATTGTACTTTTAG 57.906 33.333 0.00 0.00 0.00 1.85
2983 5808 3.593096 GTTCCCTTTACCCAACGTAGAG 58.407 50.000 0.00 0.00 0.00 2.43
3021 5846 3.416414 AGCATAGTACTGTACCCCCTT 57.584 47.619 14.05 0.00 0.00 3.95
3092 6110 2.919228 TCTCTAGCAGCTCGTGATACA 58.081 47.619 0.00 0.00 0.00 2.29
3098 6116 2.492088 AGCAGCTCGTGATACAGTTACA 59.508 45.455 0.00 0.00 0.00 2.41
3105 6123 7.860872 CAGCTCGTGATACAGTTACATATACAA 59.139 37.037 0.00 0.00 0.00 2.41
3188 6209 0.693049 ACACCCTCCATGTTGTCTCC 59.307 55.000 0.00 0.00 0.00 3.71
3218 6239 2.337583 CACGATGTAGCAATATCCCCG 58.662 52.381 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.042297 TCTGAGACATGGACTCTGGAGT 59.958 50.000 19.98 2.62 45.84 3.85
28 29 2.732763 TCTGAGACATGGACTCTGGAG 58.267 52.381 19.98 12.08 35.23 3.86
29 30 2.907458 TCTGAGACATGGACTCTGGA 57.093 50.000 19.98 15.38 35.23 3.86
30 31 4.440880 GAAATCTGAGACATGGACTCTGG 58.559 47.826 19.98 14.04 35.23 3.86
31 32 4.161942 AGGAAATCTGAGACATGGACTCTG 59.838 45.833 18.22 17.43 35.66 3.35
32 33 4.360889 AGGAAATCTGAGACATGGACTCT 58.639 43.478 18.22 4.24 35.66 3.24
33 34 4.751767 AGGAAATCTGAGACATGGACTC 57.248 45.455 13.01 13.01 35.26 3.36
34 35 5.511386 AAAGGAAATCTGAGACATGGACT 57.489 39.130 0.00 0.00 0.00 3.85
35 36 6.581171 AAAAAGGAAATCTGAGACATGGAC 57.419 37.500 0.00 0.00 0.00 4.02
60 61 9.224768 GGACTCTCCATTCCCTTGAATAAGGAA 62.225 44.444 7.62 0.00 45.30 3.36
61 62 7.830433 GGACTCTCCATTCCCTTGAATAAGGA 61.830 46.154 7.62 0.00 45.30 3.36
62 63 5.688766 GGACTCTCCATTCCCTTGAATAAGG 60.689 48.000 0.00 0.00 43.72 2.69
63 64 5.131809 AGGACTCTCCATTCCCTTGAATAAG 59.868 44.000 0.00 0.00 39.20 1.73
64 65 5.039645 AGGACTCTCCATTCCCTTGAATAA 58.960 41.667 0.00 0.00 39.20 1.40
65 66 4.635473 AGGACTCTCCATTCCCTTGAATA 58.365 43.478 0.00 0.00 39.20 1.75
66 67 3.468850 AGGACTCTCCATTCCCTTGAAT 58.531 45.455 0.00 0.00 41.96 2.57
67 68 2.921221 AGGACTCTCCATTCCCTTGAA 58.079 47.619 0.00 0.00 39.61 2.69
68 69 2.649742 AGGACTCTCCATTCCCTTGA 57.350 50.000 0.00 0.00 39.61 3.02
69 70 3.133721 CACTAGGACTCTCCATTCCCTTG 59.866 52.174 0.00 0.00 39.61 3.61
70 71 3.012959 TCACTAGGACTCTCCATTCCCTT 59.987 47.826 0.00 0.00 39.61 3.95
71 72 2.587777 TCACTAGGACTCTCCATTCCCT 59.412 50.000 0.00 0.00 39.61 4.20
72 73 3.033659 TCACTAGGACTCTCCATTCCC 57.966 52.381 0.00 0.00 39.61 3.97
73 74 4.651503 TGATTCACTAGGACTCTCCATTCC 59.348 45.833 0.00 0.00 39.61 3.01
74 75 5.127845 TGTGATTCACTAGGACTCTCCATTC 59.872 44.000 17.26 0.00 35.55 2.67
75 76 5.026121 TGTGATTCACTAGGACTCTCCATT 58.974 41.667 17.26 0.00 35.55 3.16
76 77 4.404073 GTGTGATTCACTAGGACTCTCCAT 59.596 45.833 17.26 0.00 43.13 3.41
77 78 3.764434 GTGTGATTCACTAGGACTCTCCA 59.236 47.826 17.26 0.00 43.13 3.86
78 79 4.379339 GTGTGATTCACTAGGACTCTCC 57.621 50.000 17.26 0.00 43.13 3.71
89 90 1.613437 CCCAACCCAAGTGTGATTCAC 59.387 52.381 9.93 9.93 46.46 3.18
90 91 1.496857 TCCCAACCCAAGTGTGATTCA 59.503 47.619 0.00 0.00 0.00 2.57
91 92 2.286365 TCCCAACCCAAGTGTGATTC 57.714 50.000 0.00 0.00 0.00 2.52
92 93 2.999185 ATCCCAACCCAAGTGTGATT 57.001 45.000 0.00 0.00 0.00 2.57
93 94 2.242196 CCTATCCCAACCCAAGTGTGAT 59.758 50.000 0.00 0.00 0.00 3.06
94 95 1.633432 CCTATCCCAACCCAAGTGTGA 59.367 52.381 0.00 0.00 0.00 3.58
95 96 1.633432 TCCTATCCCAACCCAAGTGTG 59.367 52.381 0.00 0.00 0.00 3.82
96 97 1.916181 CTCCTATCCCAACCCAAGTGT 59.084 52.381 0.00 0.00 0.00 3.55
97 98 2.171448 CTCTCCTATCCCAACCCAAGTG 59.829 54.545 0.00 0.00 0.00 3.16
98 99 2.482494 CTCTCCTATCCCAACCCAAGT 58.518 52.381 0.00 0.00 0.00 3.16
99 100 1.141858 GCTCTCCTATCCCAACCCAAG 59.858 57.143 0.00 0.00 0.00 3.61
100 101 1.213296 GCTCTCCTATCCCAACCCAA 58.787 55.000 0.00 0.00 0.00 4.12
101 102 0.044092 TGCTCTCCTATCCCAACCCA 59.956 55.000 0.00 0.00 0.00 4.51
102 103 0.761802 CTGCTCTCCTATCCCAACCC 59.238 60.000 0.00 0.00 0.00 4.11
103 104 0.761802 CCTGCTCTCCTATCCCAACC 59.238 60.000 0.00 0.00 0.00 3.77
104 105 0.107643 GCCTGCTCTCCTATCCCAAC 59.892 60.000 0.00 0.00 0.00 3.77
105 106 1.056700 GGCCTGCTCTCCTATCCCAA 61.057 60.000 0.00 0.00 0.00 4.12
106 107 1.460305 GGCCTGCTCTCCTATCCCA 60.460 63.158 0.00 0.00 0.00 4.37
107 108 1.152139 AGGCCTGCTCTCCTATCCC 60.152 63.158 3.11 0.00 0.00 3.85
108 109 0.470833 TGAGGCCTGCTCTCCTATCC 60.471 60.000 12.00 0.00 31.71 2.59
109 110 0.678950 GTGAGGCCTGCTCTCCTATC 59.321 60.000 12.00 0.00 31.71 2.08
110 111 1.112315 CGTGAGGCCTGCTCTCCTAT 61.112 60.000 12.00 0.00 31.71 2.57
111 112 1.754621 CGTGAGGCCTGCTCTCCTA 60.755 63.158 12.00 0.00 31.71 2.94
112 113 3.073735 CGTGAGGCCTGCTCTCCT 61.074 66.667 12.00 0.00 34.90 3.69
113 114 2.456287 AAACGTGAGGCCTGCTCTCC 62.456 60.000 12.00 0.00 0.00 3.71
114 115 0.246635 TAAACGTGAGGCCTGCTCTC 59.753 55.000 12.00 0.00 0.00 3.20
115 116 0.905357 ATAAACGTGAGGCCTGCTCT 59.095 50.000 12.00 0.00 0.00 4.09
116 117 1.739067 AATAAACGTGAGGCCTGCTC 58.261 50.000 12.00 0.00 0.00 4.26
117 118 3.560636 ATAATAAACGTGAGGCCTGCT 57.439 42.857 12.00 0.00 0.00 4.24
118 119 3.625764 TGAATAATAAACGTGAGGCCTGC 59.374 43.478 12.00 0.85 0.00 4.85
119 120 5.220854 CCTTGAATAATAAACGTGAGGCCTG 60.221 44.000 12.00 0.00 0.00 4.85
120 121 4.881850 CCTTGAATAATAAACGTGAGGCCT 59.118 41.667 3.86 3.86 0.00 5.19
121 122 4.036380 CCCTTGAATAATAAACGTGAGGCC 59.964 45.833 0.00 0.00 0.00 5.19
122 123 4.879545 TCCCTTGAATAATAAACGTGAGGC 59.120 41.667 0.00 0.00 0.00 4.70
123 124 6.346096 TCTCCCTTGAATAATAAACGTGAGG 58.654 40.000 0.00 0.00 0.00 3.86
124 125 7.265673 TCTCTCCCTTGAATAATAAACGTGAG 58.734 38.462 0.00 0.00 0.00 3.51
125 126 7.123697 TCTCTCTCCCTTGAATAATAAACGTGA 59.876 37.037 0.00 0.00 0.00 4.35
126 127 7.265673 TCTCTCTCCCTTGAATAATAAACGTG 58.734 38.462 0.00 0.00 0.00 4.49
127 128 7.342284 TCTCTCTCTCCCTTGAATAATAAACGT 59.658 37.037 0.00 0.00 0.00 3.99
128 129 7.717568 TCTCTCTCTCCCTTGAATAATAAACG 58.282 38.462 0.00 0.00 0.00 3.60
129 130 8.919145 TCTCTCTCTCTCCCTTGAATAATAAAC 58.081 37.037 0.00 0.00 0.00 2.01
130 131 9.142014 CTCTCTCTCTCTCCCTTGAATAATAAA 57.858 37.037 0.00 0.00 0.00 1.40
131 132 8.285891 ACTCTCTCTCTCTCCCTTGAATAATAA 58.714 37.037 0.00 0.00 0.00 1.40
132 133 7.821566 ACTCTCTCTCTCTCCCTTGAATAATA 58.178 38.462 0.00 0.00 0.00 0.98
133 134 6.682537 ACTCTCTCTCTCTCCCTTGAATAAT 58.317 40.000 0.00 0.00 0.00 1.28
134 135 6.086011 ACTCTCTCTCTCTCCCTTGAATAA 57.914 41.667 0.00 0.00 0.00 1.40
135 136 5.398581 GGACTCTCTCTCTCTCCCTTGAATA 60.399 48.000 0.00 0.00 0.00 1.75
136 137 4.536765 GACTCTCTCTCTCTCCCTTGAAT 58.463 47.826 0.00 0.00 0.00 2.57
137 138 3.308832 GGACTCTCTCTCTCTCCCTTGAA 60.309 52.174 0.00 0.00 0.00 2.69
138 139 2.241176 GGACTCTCTCTCTCTCCCTTGA 59.759 54.545 0.00 0.00 0.00 3.02
139 140 2.242196 AGGACTCTCTCTCTCTCCCTTG 59.758 54.545 0.00 0.00 0.00 3.61
140 141 2.573463 AGGACTCTCTCTCTCTCCCTT 58.427 52.381 0.00 0.00 0.00 3.95
141 142 2.286935 AGGACTCTCTCTCTCTCCCT 57.713 55.000 0.00 0.00 0.00 4.20
142 143 4.398319 CATTAGGACTCTCTCTCTCTCCC 58.602 52.174 0.00 0.00 0.00 4.30
143 144 4.104102 TCCATTAGGACTCTCTCTCTCTCC 59.896 50.000 0.00 0.00 39.61 3.71
144 145 5.304686 TCCATTAGGACTCTCTCTCTCTC 57.695 47.826 0.00 0.00 39.61 3.20
145 146 5.725551 TTCCATTAGGACTCTCTCTCTCT 57.274 43.478 0.00 0.00 45.73 3.10
146 147 6.569780 GTTTTCCATTAGGACTCTCTCTCTC 58.430 44.000 0.00 0.00 45.73 3.20
147 148 5.126384 CGTTTTCCATTAGGACTCTCTCTCT 59.874 44.000 0.00 0.00 45.73 3.10
148 149 5.125739 TCGTTTTCCATTAGGACTCTCTCTC 59.874 44.000 0.00 0.00 45.73 3.20
149 150 5.017490 TCGTTTTCCATTAGGACTCTCTCT 58.983 41.667 0.00 0.00 45.73 3.10
150 151 5.103687 GTCGTTTTCCATTAGGACTCTCTC 58.896 45.833 0.00 0.00 45.73 3.20
151 152 4.773149 AGTCGTTTTCCATTAGGACTCTCT 59.227 41.667 0.00 0.00 45.73 3.10
152 153 5.074584 AGTCGTTTTCCATTAGGACTCTC 57.925 43.478 0.00 0.00 45.73 3.20
153 154 5.074584 GAGTCGTTTTCCATTAGGACTCT 57.925 43.478 14.30 0.00 45.73 3.24
155 156 5.221661 ACAAGAGTCGTTTTCCATTAGGACT 60.222 40.000 0.00 0.00 45.73 3.85
156 157 4.995487 ACAAGAGTCGTTTTCCATTAGGAC 59.005 41.667 0.00 0.00 45.73 3.85
157 158 5.223449 ACAAGAGTCGTTTTCCATTAGGA 57.777 39.130 0.00 0.00 43.93 2.94
158 159 6.395629 TCTACAAGAGTCGTTTTCCATTAGG 58.604 40.000 0.00 0.00 0.00 2.69
159 160 7.010552 CCATCTACAAGAGTCGTTTTCCATTAG 59.989 40.741 0.00 0.00 0.00 1.73
160 161 6.816640 CCATCTACAAGAGTCGTTTTCCATTA 59.183 38.462 0.00 0.00 0.00 1.90
161 162 5.643777 CCATCTACAAGAGTCGTTTTCCATT 59.356 40.000 0.00 0.00 0.00 3.16
162 163 5.178797 CCATCTACAAGAGTCGTTTTCCAT 58.821 41.667 0.00 0.00 0.00 3.41
163 164 4.562757 CCCATCTACAAGAGTCGTTTTCCA 60.563 45.833 0.00 0.00 0.00 3.53
164 165 3.933332 CCCATCTACAAGAGTCGTTTTCC 59.067 47.826 0.00 0.00 0.00 3.13
165 166 4.817517 TCCCATCTACAAGAGTCGTTTTC 58.182 43.478 0.00 0.00 0.00 2.29
166 167 4.884668 TCCCATCTACAAGAGTCGTTTT 57.115 40.909 0.00 0.00 0.00 2.43
167 168 6.380274 TCTTATCCCATCTACAAGAGTCGTTT 59.620 38.462 0.00 0.00 0.00 3.60
168 169 5.892119 TCTTATCCCATCTACAAGAGTCGTT 59.108 40.000 0.00 0.00 0.00 3.85
169 170 5.446860 TCTTATCCCATCTACAAGAGTCGT 58.553 41.667 0.00 0.00 0.00 4.34
170 171 5.765677 TCTCTTATCCCATCTACAAGAGTCG 59.234 44.000 8.91 0.00 41.79 4.18
171 172 6.294508 GCTCTCTTATCCCATCTACAAGAGTC 60.295 46.154 8.91 0.00 41.79 3.36
172 173 5.538433 GCTCTCTTATCCCATCTACAAGAGT 59.462 44.000 8.91 0.00 41.79 3.24
173 174 5.538053 TGCTCTCTTATCCCATCTACAAGAG 59.462 44.000 3.76 3.76 42.24 2.85
174 175 5.303078 GTGCTCTCTTATCCCATCTACAAGA 59.697 44.000 0.00 0.00 0.00 3.02
175 176 5.537188 GTGCTCTCTTATCCCATCTACAAG 58.463 45.833 0.00 0.00 0.00 3.16
176 177 4.038042 CGTGCTCTCTTATCCCATCTACAA 59.962 45.833 0.00 0.00 0.00 2.41
177 178 3.570125 CGTGCTCTCTTATCCCATCTACA 59.430 47.826 0.00 0.00 0.00 2.74
178 179 3.612955 GCGTGCTCTCTTATCCCATCTAC 60.613 52.174 0.00 0.00 0.00 2.59
179 180 2.558795 GCGTGCTCTCTTATCCCATCTA 59.441 50.000 0.00 0.00 0.00 1.98
180 181 1.342819 GCGTGCTCTCTTATCCCATCT 59.657 52.381 0.00 0.00 0.00 2.90
181 182 1.606737 GGCGTGCTCTCTTATCCCATC 60.607 57.143 0.00 0.00 0.00 3.51
182 183 0.394565 GGCGTGCTCTCTTATCCCAT 59.605 55.000 0.00 0.00 0.00 4.00
183 184 0.687757 AGGCGTGCTCTCTTATCCCA 60.688 55.000 0.00 0.00 0.00 4.37
184 185 0.032815 GAGGCGTGCTCTCTTATCCC 59.967 60.000 0.00 0.00 0.00 3.85
185 186 0.747255 TGAGGCGTGCTCTCTTATCC 59.253 55.000 10.32 0.00 32.78 2.59
186 187 1.846541 GTGAGGCGTGCTCTCTTATC 58.153 55.000 10.32 0.00 32.78 1.75
187 188 0.101399 CGTGAGGCGTGCTCTCTTAT 59.899 55.000 10.32 0.00 35.54 1.73
188 189 1.506718 CGTGAGGCGTGCTCTCTTA 59.493 57.895 10.32 0.00 35.54 2.10
189 190 2.259818 CGTGAGGCGTGCTCTCTT 59.740 61.111 10.32 0.00 35.54 2.85
190 191 4.427661 GCGTGAGGCGTGCTCTCT 62.428 66.667 10.32 0.00 43.66 3.10
199 200 1.098050 ATTGGATGAAAGCGTGAGGC 58.902 50.000 0.00 0.00 44.05 4.70
200 201 1.402968 CCATTGGATGAAAGCGTGAGG 59.597 52.381 0.00 0.00 0.00 3.86
201 202 1.202222 GCCATTGGATGAAAGCGTGAG 60.202 52.381 6.95 0.00 0.00 3.51
202 203 0.810648 GCCATTGGATGAAAGCGTGA 59.189 50.000 6.95 0.00 0.00 4.35
203 204 0.813184 AGCCATTGGATGAAAGCGTG 59.187 50.000 6.95 0.00 0.00 5.34
204 205 2.017049 GTAGCCATTGGATGAAAGCGT 58.983 47.619 6.95 0.00 0.00 5.07
205 206 2.016318 TGTAGCCATTGGATGAAAGCG 58.984 47.619 6.95 0.00 0.00 4.68
206 207 4.454728 TTTGTAGCCATTGGATGAAAGC 57.545 40.909 6.95 0.00 0.00 3.51
207 208 7.099266 TGTATTTGTAGCCATTGGATGAAAG 57.901 36.000 6.95 0.00 0.00 2.62
208 209 7.658525 ATGTATTTGTAGCCATTGGATGAAA 57.341 32.000 6.95 4.73 0.00 2.69
209 210 7.658525 AATGTATTTGTAGCCATTGGATGAA 57.341 32.000 6.95 0.00 0.00 2.57
210 211 8.938801 ATAATGTATTTGTAGCCATTGGATGA 57.061 30.769 6.95 0.00 0.00 2.92
238 239 9.855021 CTAAAGAAAATTGACCGTCCATTTAAT 57.145 29.630 10.19 1.60 0.00 1.40
239 240 8.852135 ACTAAAGAAAATTGACCGTCCATTTAA 58.148 29.630 10.19 0.00 0.00 1.52
240 241 8.398878 ACTAAAGAAAATTGACCGTCCATTTA 57.601 30.769 10.19 0.00 0.00 1.40
241 242 7.284919 ACTAAAGAAAATTGACCGTCCATTT 57.715 32.000 5.03 5.03 0.00 2.32
242 243 6.894339 ACTAAAGAAAATTGACCGTCCATT 57.106 33.333 0.00 0.00 0.00 3.16
243 244 6.894339 AACTAAAGAAAATTGACCGTCCAT 57.106 33.333 0.00 0.00 0.00 3.41
244 245 6.319152 TGAAACTAAAGAAAATTGACCGTCCA 59.681 34.615 0.00 0.00 0.00 4.02
245 246 6.635641 GTGAAACTAAAGAAAATTGACCGTCC 59.364 38.462 0.00 0.00 0.00 4.79
246 247 6.356190 CGTGAAACTAAAGAAAATTGACCGTC 59.644 38.462 0.00 0.00 31.75 4.79
247 248 6.196571 CGTGAAACTAAAGAAAATTGACCGT 58.803 36.000 0.00 0.00 31.75 4.83
248 249 5.623673 CCGTGAAACTAAAGAAAATTGACCG 59.376 40.000 0.00 0.00 31.75 4.79
249 250 6.500910 ACCGTGAAACTAAAGAAAATTGACC 58.499 36.000 0.00 0.00 31.75 4.02
250 251 7.980742 AACCGTGAAACTAAAGAAAATTGAC 57.019 32.000 0.00 0.00 31.75 3.18
255 256 9.291664 CACATTAAACCGTGAAACTAAAGAAAA 57.708 29.630 0.00 0.00 35.02 2.29
256 257 7.916450 CCACATTAAACCGTGAAACTAAAGAAA 59.084 33.333 4.99 0.00 35.02 2.52
257 258 7.067251 ACCACATTAAACCGTGAAACTAAAGAA 59.933 33.333 4.99 0.00 35.02 2.52
258 259 6.543100 ACCACATTAAACCGTGAAACTAAAGA 59.457 34.615 4.99 0.00 35.02 2.52
259 260 6.635239 CACCACATTAAACCGTGAAACTAAAG 59.365 38.462 4.99 0.00 35.02 1.85
260 261 6.095160 ACACCACATTAAACCGTGAAACTAAA 59.905 34.615 4.99 0.00 35.02 1.85
261 262 5.589452 ACACCACATTAAACCGTGAAACTAA 59.411 36.000 4.99 0.00 35.02 2.24
262 263 5.124645 ACACCACATTAAACCGTGAAACTA 58.875 37.500 4.99 0.00 35.02 2.24
263 264 3.949113 ACACCACATTAAACCGTGAAACT 59.051 39.130 4.99 0.00 35.02 2.66
264 265 4.035909 AGACACCACATTAAACCGTGAAAC 59.964 41.667 4.99 0.00 35.02 2.78
265 266 4.200874 AGACACCACATTAAACCGTGAAA 58.799 39.130 4.99 0.00 35.02 2.69
266 267 3.810941 GAGACACCACATTAAACCGTGAA 59.189 43.478 4.99 0.00 35.02 3.18
267 268 3.395639 GAGACACCACATTAAACCGTGA 58.604 45.455 4.99 0.00 35.02 4.35
268 269 2.156891 CGAGACACCACATTAAACCGTG 59.843 50.000 0.00 0.00 0.00 4.94
269 270 2.224113 ACGAGACACCACATTAAACCGT 60.224 45.455 0.00 0.00 0.00 4.83
270 271 2.409975 ACGAGACACCACATTAAACCG 58.590 47.619 0.00 0.00 0.00 4.44
271 272 4.331717 CCATACGAGACACCACATTAAACC 59.668 45.833 0.00 0.00 0.00 3.27
272 273 4.933400 ACCATACGAGACACCACATTAAAC 59.067 41.667 0.00 0.00 0.00 2.01
273 274 4.932799 CACCATACGAGACACCACATTAAA 59.067 41.667 0.00 0.00 0.00 1.52
274 275 4.500127 CACCATACGAGACACCACATTAA 58.500 43.478 0.00 0.00 0.00 1.40
275 276 3.677700 GCACCATACGAGACACCACATTA 60.678 47.826 0.00 0.00 0.00 1.90
276 277 2.935238 GCACCATACGAGACACCACATT 60.935 50.000 0.00 0.00 0.00 2.71
277 278 1.405526 GCACCATACGAGACACCACAT 60.406 52.381 0.00 0.00 0.00 3.21
278 279 0.037697 GCACCATACGAGACACCACA 60.038 55.000 0.00 0.00 0.00 4.17
279 280 0.739813 GGCACCATACGAGACACCAC 60.740 60.000 0.00 0.00 0.00 4.16
280 281 0.902984 AGGCACCATACGAGACACCA 60.903 55.000 0.00 0.00 0.00 4.17
281 282 0.249398 AAGGCACCATACGAGACACC 59.751 55.000 0.00 0.00 0.00 4.16
282 283 1.067142 TGAAGGCACCATACGAGACAC 60.067 52.381 0.00 0.00 0.00 3.67
283 284 1.262417 TGAAGGCACCATACGAGACA 58.738 50.000 0.00 0.00 0.00 3.41
284 285 2.380084 TTGAAGGCACCATACGAGAC 57.620 50.000 0.00 0.00 0.00 3.36
285 286 3.627395 AATTGAAGGCACCATACGAGA 57.373 42.857 0.00 0.00 0.00 4.04
286 287 4.442706 ACTAATTGAAGGCACCATACGAG 58.557 43.478 0.00 0.00 0.00 4.18
287 288 4.481368 ACTAATTGAAGGCACCATACGA 57.519 40.909 0.00 0.00 0.00 3.43
288 289 6.671614 TTTACTAATTGAAGGCACCATACG 57.328 37.500 0.00 0.00 0.00 3.06
311 312 8.470805 CGTCCTACAGGCAATCTTATCTTATAT 58.529 37.037 0.00 0.00 34.44 0.86
312 313 7.450634 ACGTCCTACAGGCAATCTTATCTTATA 59.549 37.037 0.00 0.00 34.44 0.98
313 314 6.267928 ACGTCCTACAGGCAATCTTATCTTAT 59.732 38.462 0.00 0.00 34.44 1.73
314 315 5.597182 ACGTCCTACAGGCAATCTTATCTTA 59.403 40.000 0.00 0.00 34.44 2.10
315 316 4.406003 ACGTCCTACAGGCAATCTTATCTT 59.594 41.667 0.00 0.00 34.44 2.40
316 317 3.961408 ACGTCCTACAGGCAATCTTATCT 59.039 43.478 0.00 0.00 34.44 1.98
317 318 4.051922 CACGTCCTACAGGCAATCTTATC 58.948 47.826 0.00 0.00 34.44 1.75
330 331 2.981859 ATGTTGGGATCACGTCCTAC 57.018 50.000 0.00 0.00 46.91 3.18
729 2567 4.400567 GCCATTCAGCAGAATAGTTTCCTT 59.599 41.667 3.79 0.00 42.46 3.36
1798 4620 2.699846 TCAACTGCTTTTTCATGCCCTT 59.300 40.909 0.00 0.00 0.00 3.95
1859 4681 2.017049 GGCAGTACCAATTGCTTCGAT 58.983 47.619 0.00 0.00 38.35 3.59
1931 4753 4.080807 TCCAGGTAATTGCGTTTCTGGATA 60.081 41.667 12.86 0.00 40.72 2.59
2094 4916 0.755079 TCTCTGCTGCTGTTGTCAGT 59.245 50.000 0.00 0.00 43.05 3.41
2096 4918 0.250038 GGTCTCTGCTGCTGTTGTCA 60.250 55.000 0.00 0.00 0.00 3.58
2101 4923 2.203082 TCACGGTCTCTGCTGCTGT 61.203 57.895 0.00 0.00 0.00 4.40
2289 5111 0.033503 TCCACGCCATAGACCTCTCA 60.034 55.000 0.00 0.00 0.00 3.27
2356 5178 1.271543 TGGTTGAAGTCATGCTGGGAG 60.272 52.381 0.00 0.00 0.00 4.30
2434 5256 1.446966 GTCGAGCTCCAGGTCTTGC 60.447 63.158 8.47 0.00 40.17 4.01
2555 5377 1.496429 GTCTGAATGGATGACCCCCAT 59.504 52.381 0.00 0.00 45.75 4.00
2861 5683 4.196193 TCGAATCACCACACAGAAAAGTT 58.804 39.130 0.00 0.00 0.00 2.66
2862 5684 3.804036 TCGAATCACCACACAGAAAAGT 58.196 40.909 0.00 0.00 0.00 2.66
2902 5724 7.971722 ACACACAGTCCACAAAGTAAAATAAAC 59.028 33.333 0.00 0.00 0.00 2.01
3002 5827 3.036091 TGAAGGGGGTACAGTACTATGC 58.964 50.000 10.62 0.00 0.00 3.14
3021 5846 5.768662 TGGATACACCGGTAAAACAAAATGA 59.231 36.000 6.87 0.00 46.17 2.57
3092 6110 9.569122 ACTTGTCCAAAACTTGTATATGTAACT 57.431 29.630 0.00 0.00 0.00 2.24
3105 6123 6.909550 TTTGCCATATACTTGTCCAAAACT 57.090 33.333 0.00 0.00 0.00 2.66
3188 6209 1.438651 CTACATCGTGGTGGTGGTTG 58.561 55.000 0.00 0.00 0.00 3.77
3218 6239 3.695830 TGGTTACAACTCTCCATCACC 57.304 47.619 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.