Multiple sequence alignment - TraesCS1A01G438300

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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 TraesCS1A01G438300 chr1A 100.000 3235 0 0 1 3235 588020684 588017450 0.000000e+00 5975.0
1 TraesCS1A01G438300 chr1A 95.588 1836 54 10 1415 3235 588119236 588117413 0.000000e+00 2916.0
2 TraesCS1A01G438300 chr1A 84.046 351 30 14 520 870 588123862 588123538 6.740000e-82 315.0
3 TraesCS1A01G438300 chr1A 92.857 140 10 0 1110 1249 588119889 588119750 1.520000e-48 204.0
4 TraesCS1A01G438300 chr1A 84.444 180 22 4 336 512 588124388 588124212 4.290000e-39 172.0
5 TraesCS1A01G438300 chr1D 89.074 1858 105 47 514 2320 490104163 490105973 0.000000e+00 2217.0
6 TraesCS1A01G438300 chr1D 90.787 1563 72 18 1415 2948 488777483 488775964 0.000000e+00 2023.0
7 TraesCS1A01G438300 chr1D 90.325 1385 77 19 1400 2765 489106371 489107717 0.000000e+00 1762.0
8 TraesCS1A01G438300 chr1D 87.340 624 34 13 2318 2913 490118465 490119071 0.000000e+00 673.0
9 TraesCS1A01G438300 chr1D 93.631 314 13 5 514 826 490103265 490103572 2.270000e-126 462.0
10 TraesCS1A01G438300 chr1D 94.604 278 15 0 2910 3187 490119151 490119428 6.410000e-117 431.0
11 TraesCS1A01G438300 chr1D 86.849 403 30 14 514 903 489105005 489105397 2.310000e-116 429.0
12 TraesCS1A01G438300 chr1D 90.496 242 16 4 1 239 490098320 490098557 2.420000e-81 313.0
13 TraesCS1A01G438300 chr1D 85.944 249 15 8 1110 1349 489105716 489105953 6.930000e-62 248.0
14 TraesCS1A01G438300 chr1D 95.833 144 6 0 349 492 490103573 490103716 1.940000e-57 233.0
15 TraesCS1A01G438300 chr1D 88.304 171 9 3 336 496 489104499 489104668 9.160000e-46 195.0
16 TraesCS1A01G438300 chr1D 79.352 247 34 10 2132 2363 488951017 488951261 1.200000e-34 158.0
17 TraesCS1A01G438300 chr1D 92.647 68 5 0 2517 2584 488951315 488951382 7.390000e-17 99.0
18 TraesCS1A01G438300 chr1D 100.000 29 0 0 2611 2639 488776394 488776366 2.000000e-03 54.7
19 TraesCS1A01G438300 chr1B 94.737 1159 37 7 1809 2967 680977714 680978848 0.000000e+00 1781.0
20 TraesCS1A01G438300 chr1B 87.955 357 33 5 514 870 680967175 680967521 2.320000e-111 412.0
21 TraesCS1A01G438300 chr1B 90.278 216 11 2 1415 1628 680977444 680977651 1.140000e-69 274.0
22 TraesCS1A01G438300 chr1B 87.200 250 15 5 1110 1349 680976821 680977063 5.320000e-68 268.0
23 TraesCS1A01G438300 chr1B 97.945 146 3 0 3090 3235 680980340 680980485 1.490000e-63 254.0
24 TraesCS1A01G438300 chr1B 83.582 201 10 11 336 524 680966608 680966797 2.000000e-37 167.0
25 TraesCS1A01G438300 chr1B 100.000 54 0 0 3050 3103 680978847 680978900 2.050000e-17 100.0
26 TraesCS1A01G438300 chr2A 78.261 230 31 9 89 315 768258859 768258646 2.620000e-26 130.0
27 TraesCS1A01G438300 chr7A 78.199 211 32 11 109 308 95222773 95222980 4.380000e-24 122.0
28 TraesCS1A01G438300 chr6A 82.609 115 16 4 118 229 115981277 115981164 7.390000e-17 99.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G438300 chr1A 588017450 588020684 3234 True 5975.000000 5975 100.00000 1 3235 1 chr1A.!!$R1 3234
1 TraesCS1A01G438300 chr1A 588117413 588124388 6975 True 901.750000 2916 89.23375 336 3235 4 chr1A.!!$R2 2899
2 TraesCS1A01G438300 chr1D 488775964 488777483 1519 True 1038.850000 2023 95.39350 1415 2948 2 chr1D.!!$R1 1533
3 TraesCS1A01G438300 chr1D 490103265 490105973 2708 False 970.666667 2217 92.84600 349 2320 3 chr1D.!!$F4 1971
4 TraesCS1A01G438300 chr1D 489104499 489107717 3218 False 658.500000 1762 87.85550 336 2765 4 chr1D.!!$F3 2429
5 TraesCS1A01G438300 chr1D 490118465 490119428 963 False 552.000000 673 90.97200 2318 3187 2 chr1D.!!$F5 869
6 TraesCS1A01G438300 chr1B 680976821 680980485 3664 False 535.400000 1781 94.03200 1110 3235 5 chr1B.!!$F2 2125
7 TraesCS1A01G438300 chr1B 680966608 680967521 913 False 289.500000 412 85.76850 336 870 2 chr1B.!!$F1 534

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
965 4796 0.179029 CCTCTCCCTCTCTCGAGTCC 60.179 65.0 13.13 0.00 35.43 3.85 F
1482 5842 0.034089 GTACCTGGCTGCCTGGAAAT 60.034 55.0 40.53 25.64 44.09 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2027 6433 0.321346 TCTCAGCCGAATGAGTTGCA 59.679 50.000 14.14 0.0 45.7 4.08 R
2716 7137 1.396301 CAAAGAGCTCGCACATCCTTC 59.604 52.381 8.37 0.0 0.0 3.46 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
22 23 5.382573 GCTTTATCTAACGTCAGCTTCTG 57.617 43.478 0.00 0.00 0.00 3.02
23 24 4.865365 GCTTTATCTAACGTCAGCTTCTGT 59.135 41.667 0.00 0.00 32.61 3.41
24 25 5.348997 GCTTTATCTAACGTCAGCTTCTGTT 59.651 40.000 0.00 0.00 32.61 3.16
25 26 6.530534 GCTTTATCTAACGTCAGCTTCTGTTA 59.469 38.462 0.00 0.00 32.61 2.41
26 27 7.253817 GCTTTATCTAACGTCAGCTTCTGTTAG 60.254 40.741 16.93 16.93 43.12 2.34
27 28 4.436242 TCTAACGTCAGCTTCTGTTAGG 57.564 45.455 20.33 8.92 42.41 2.69
31 32 3.805207 ACGTCAGCTTCTGTTAGGTTTT 58.195 40.909 0.00 0.00 32.61 2.43
33 34 5.548406 ACGTCAGCTTCTGTTAGGTTTTAT 58.452 37.500 0.00 0.00 32.61 1.40
34 35 5.638234 ACGTCAGCTTCTGTTAGGTTTTATC 59.362 40.000 0.00 0.00 32.61 1.75
35 36 5.063564 CGTCAGCTTCTGTTAGGTTTTATCC 59.936 44.000 0.00 0.00 32.61 2.59
36 37 5.063564 GTCAGCTTCTGTTAGGTTTTATCCG 59.936 44.000 0.00 0.00 32.61 4.18
37 38 5.046878 TCAGCTTCTGTTAGGTTTTATCCGA 60.047 40.000 0.00 0.00 32.61 4.55
38 39 5.817816 CAGCTTCTGTTAGGTTTTATCCGAT 59.182 40.000 0.00 0.00 0.00 4.18
39 40 6.018669 CAGCTTCTGTTAGGTTTTATCCGATC 60.019 42.308 0.00 0.00 0.00 3.69
41 42 4.940463 TCTGTTAGGTTTTATCCGATCGG 58.060 43.478 28.62 28.62 0.00 4.18
42 43 4.056050 CTGTTAGGTTTTATCCGATCGGG 58.944 47.826 32.79 15.22 35.59 5.14
43 44 3.451902 TGTTAGGTTTTATCCGATCGGGT 59.548 43.478 32.79 29.42 37.00 5.28
44 45 4.080975 TGTTAGGTTTTATCCGATCGGGTT 60.081 41.667 32.79 22.42 37.00 4.11
45 46 2.914059 AGGTTTTATCCGATCGGGTTG 58.086 47.619 32.79 8.59 37.00 3.77
46 47 1.332686 GGTTTTATCCGATCGGGTTGC 59.667 52.381 32.79 16.23 37.00 4.17
47 48 2.011222 GTTTTATCCGATCGGGTTGCA 58.989 47.619 32.79 14.74 37.00 4.08
48 49 1.658994 TTTATCCGATCGGGTTGCAC 58.341 50.000 32.79 0.00 37.00 4.57
49 50 0.528901 TTATCCGATCGGGTTGCACG 60.529 55.000 32.79 5.84 37.00 5.34
50 51 1.669049 TATCCGATCGGGTTGCACGT 61.669 55.000 32.79 11.73 37.00 4.49
51 52 3.487202 CCGATCGGGTTGCACGTG 61.487 66.667 26.95 12.28 0.00 4.49
53 54 2.314647 CGATCGGGTTGCACGTGTT 61.315 57.895 18.38 0.00 0.00 3.32
55 56 1.149987 GATCGGGTTGCACGTGTTAA 58.850 50.000 18.38 10.23 0.00 2.01
56 57 1.532007 GATCGGGTTGCACGTGTTAAA 59.468 47.619 18.38 6.88 0.00 1.52
58 59 1.741706 TCGGGTTGCACGTGTTAAAAA 59.258 42.857 18.38 1.75 0.00 1.94
59 60 2.358267 TCGGGTTGCACGTGTTAAAAAT 59.642 40.909 18.38 0.00 0.00 1.82
61 62 4.215827 TCGGGTTGCACGTGTTAAAAATAT 59.784 37.500 18.38 0.00 0.00 1.28
62 63 4.322274 CGGGTTGCACGTGTTAAAAATATG 59.678 41.667 18.38 0.00 0.00 1.78
63 64 4.623595 GGGTTGCACGTGTTAAAAATATGG 59.376 41.667 18.38 0.00 0.00 2.74
66 67 4.079970 TGCACGTGTTAAAAATATGGGGA 58.920 39.130 18.38 0.00 0.00 4.81
67 68 4.707448 TGCACGTGTTAAAAATATGGGGAT 59.293 37.500 18.38 0.00 0.00 3.85
68 69 5.040635 GCACGTGTTAAAAATATGGGGATG 58.959 41.667 18.38 0.00 0.00 3.51
69 70 5.040635 CACGTGTTAAAAATATGGGGATGC 58.959 41.667 7.58 0.00 0.00 3.91
70 71 4.953579 ACGTGTTAAAAATATGGGGATGCT 59.046 37.500 0.00 0.00 0.00 3.79
71 72 5.420739 ACGTGTTAAAAATATGGGGATGCTT 59.579 36.000 0.00 0.00 0.00 3.91
73 74 7.138736 CGTGTTAAAAATATGGGGATGCTTAG 58.861 38.462 0.00 0.00 0.00 2.18
74 75 7.433680 GTGTTAAAAATATGGGGATGCTTAGG 58.566 38.462 0.00 0.00 0.00 2.69
75 76 7.286775 GTGTTAAAAATATGGGGATGCTTAGGA 59.713 37.037 0.00 0.00 0.00 2.94
76 77 7.505585 TGTTAAAAATATGGGGATGCTTAGGAG 59.494 37.037 0.00 0.00 0.00 3.69
77 78 4.664688 AAATATGGGGATGCTTAGGAGG 57.335 45.455 0.00 0.00 0.00 4.30
78 79 1.362224 TATGGGGATGCTTAGGAGGC 58.638 55.000 0.00 0.00 0.00 4.70
79 80 0.698886 ATGGGGATGCTTAGGAGGCA 60.699 55.000 0.00 0.00 44.05 4.75
80 81 1.348008 TGGGGATGCTTAGGAGGCAG 61.348 60.000 0.00 0.00 43.15 4.85
81 82 1.056700 GGGGATGCTTAGGAGGCAGA 61.057 60.000 0.00 0.00 43.15 4.26
83 84 0.249657 GGATGCTTAGGAGGCAGACG 60.250 60.000 0.00 0.00 43.15 4.18
86 87 1.195115 TGCTTAGGAGGCAGACGATT 58.805 50.000 0.00 0.00 34.56 3.34
87 88 1.134699 TGCTTAGGAGGCAGACGATTG 60.135 52.381 0.00 0.00 34.56 2.67
88 89 1.137086 GCTTAGGAGGCAGACGATTGA 59.863 52.381 0.00 0.00 0.00 2.57
90 91 3.861840 CTTAGGAGGCAGACGATTGAAA 58.138 45.455 0.00 0.00 0.00 2.69
91 92 4.446371 CTTAGGAGGCAGACGATTGAAAT 58.554 43.478 0.00 0.00 0.00 2.17
92 93 3.356529 AGGAGGCAGACGATTGAAATT 57.643 42.857 0.00 0.00 0.00 1.82
93 94 3.690460 AGGAGGCAGACGATTGAAATTT 58.310 40.909 0.00 0.00 0.00 1.82
94 95 3.691609 AGGAGGCAGACGATTGAAATTTC 59.308 43.478 11.41 11.41 0.00 2.17
105 106 6.075280 ACGATTGAAATTTCGTTTTAGGTCG 58.925 36.000 13.34 13.80 45.62 4.79
106 107 5.506832 CGATTGAAATTTCGTTTTAGGTCGG 59.493 40.000 13.34 0.00 29.73 4.79
107 108 6.563222 ATTGAAATTTCGTTTTAGGTCGGA 57.437 33.333 13.34 0.00 0.00 4.55
109 110 5.299148 TGAAATTTCGTTTTAGGTCGGAGA 58.701 37.500 13.34 0.00 0.00 3.71
110 111 5.759273 TGAAATTTCGTTTTAGGTCGGAGAA 59.241 36.000 13.34 0.00 39.69 2.87
111 112 6.428771 TGAAATTTCGTTTTAGGTCGGAGAAT 59.571 34.615 13.34 0.00 39.69 2.40
112 113 6.418585 AATTTCGTTTTAGGTCGGAGAATC 57.581 37.500 0.00 0.00 39.69 2.52
116 117 3.991773 CGTTTTAGGTCGGAGAATCAACA 59.008 43.478 0.00 0.00 39.69 3.33
117 118 4.630069 CGTTTTAGGTCGGAGAATCAACAT 59.370 41.667 0.00 0.00 39.69 2.71
118 119 5.445939 CGTTTTAGGTCGGAGAATCAACATG 60.446 44.000 0.00 0.00 39.69 3.21
122 123 2.352960 GGTCGGAGAATCAACATGAAGC 59.647 50.000 0.00 0.00 39.69 3.86
123 124 2.029728 GTCGGAGAATCAACATGAAGCG 59.970 50.000 0.00 0.00 39.69 4.68
124 125 2.002586 CGGAGAATCAACATGAAGCGT 58.997 47.619 0.00 0.00 36.25 5.07
126 127 3.616821 CGGAGAATCAACATGAAGCGTTA 59.383 43.478 0.00 0.00 36.25 3.18
128 129 4.870426 GGAGAATCAACATGAAGCGTTAGA 59.130 41.667 0.00 0.00 36.25 2.10
129 130 5.525378 GGAGAATCAACATGAAGCGTTAGAT 59.475 40.000 0.00 0.00 36.25 1.98
134 135 9.554724 GAATCAACATGAAGCGTTAGATAAAAA 57.445 29.630 0.00 0.00 0.00 1.94
152 153 4.817318 AAAAACCAATGCACCGGATAAT 57.183 36.364 9.46 0.00 0.00 1.28
153 154 4.385358 AAAACCAATGCACCGGATAATC 57.615 40.909 9.46 0.00 0.00 1.75
154 155 3.297134 AACCAATGCACCGGATAATCT 57.703 42.857 9.46 0.00 0.00 2.40
155 156 2.851195 ACCAATGCACCGGATAATCTC 58.149 47.619 9.46 0.00 0.00 2.75
156 157 2.439507 ACCAATGCACCGGATAATCTCT 59.560 45.455 9.46 0.00 0.00 3.10
158 159 3.499918 CCAATGCACCGGATAATCTCTTC 59.500 47.826 9.46 0.00 0.00 2.87
159 160 4.384056 CAATGCACCGGATAATCTCTTCT 58.616 43.478 9.46 0.00 0.00 2.85
162 163 3.321111 TGCACCGGATAATCTCTTCTACC 59.679 47.826 9.46 0.00 0.00 3.18
163 164 3.574826 GCACCGGATAATCTCTTCTACCT 59.425 47.826 9.46 0.00 0.00 3.08
164 165 4.321378 GCACCGGATAATCTCTTCTACCTC 60.321 50.000 9.46 0.00 0.00 3.85
166 167 4.202440 ACCGGATAATCTCTTCTACCTCGA 60.202 45.833 9.46 0.00 0.00 4.04
167 168 4.760715 CCGGATAATCTCTTCTACCTCGAA 59.239 45.833 0.00 0.00 0.00 3.71
168 169 5.416326 CCGGATAATCTCTTCTACCTCGAAT 59.584 44.000 0.00 0.00 0.00 3.34
169 170 6.071840 CCGGATAATCTCTTCTACCTCGAATT 60.072 42.308 0.00 0.00 0.00 2.17
170 171 6.804295 CGGATAATCTCTTCTACCTCGAATTG 59.196 42.308 0.00 0.00 0.00 2.32
171 172 7.522399 CGGATAATCTCTTCTACCTCGAATTGT 60.522 40.741 0.00 0.00 0.00 2.71
172 173 8.145122 GGATAATCTCTTCTACCTCGAATTGTT 58.855 37.037 0.00 0.00 0.00 2.83
173 174 9.535878 GATAATCTCTTCTACCTCGAATTGTTT 57.464 33.333 0.00 0.00 0.00 2.83
174 175 7.602517 AATCTCTTCTACCTCGAATTGTTTG 57.397 36.000 0.00 0.00 0.00 2.93
175 176 6.097915 TCTCTTCTACCTCGAATTGTTTGT 57.902 37.500 0.00 0.00 0.00 2.83
176 177 6.522054 TCTCTTCTACCTCGAATTGTTTGTT 58.478 36.000 0.00 0.00 0.00 2.83
177 178 6.645415 TCTCTTCTACCTCGAATTGTTTGTTC 59.355 38.462 0.00 0.00 0.00 3.18
178 179 5.699458 TCTTCTACCTCGAATTGTTTGTTCC 59.301 40.000 0.00 0.00 0.00 3.62
180 181 4.994852 TCTACCTCGAATTGTTTGTTCCTG 59.005 41.667 0.00 0.00 0.00 3.86
181 182 2.884639 ACCTCGAATTGTTTGTTCCTGG 59.115 45.455 0.00 0.00 0.00 4.45
182 183 3.146066 CCTCGAATTGTTTGTTCCTGGA 58.854 45.455 0.00 0.00 0.00 3.86
183 184 3.568007 CCTCGAATTGTTTGTTCCTGGAA 59.432 43.478 4.68 4.68 0.00 3.53
184 185 4.037446 CCTCGAATTGTTTGTTCCTGGAAA 59.963 41.667 11.40 0.00 0.00 3.13
191 192 6.783708 TTGTTTGTTCCTGGAAACAATAGT 57.216 33.333 17.11 0.00 45.70 2.12
192 193 6.783708 TGTTTGTTCCTGGAAACAATAGTT 57.216 33.333 11.40 0.00 45.70 2.24
193 194 6.801575 TGTTTGTTCCTGGAAACAATAGTTC 58.198 36.000 11.40 0.00 45.70 3.01
194 195 6.183360 TGTTTGTTCCTGGAAACAATAGTTCC 60.183 38.462 11.40 0.00 45.70 3.62
195 196 4.403734 TGTTCCTGGAAACAATAGTTCCC 58.596 43.478 11.40 0.00 42.06 3.97
196 197 4.105697 TGTTCCTGGAAACAATAGTTCCCT 59.894 41.667 11.40 0.00 42.06 4.20
197 198 4.301072 TCCTGGAAACAATAGTTCCCTG 57.699 45.455 0.00 0.00 42.06 4.45
198 199 3.356290 CCTGGAAACAATAGTTCCCTGG 58.644 50.000 0.92 0.00 43.01 4.45
199 200 3.245264 CCTGGAAACAATAGTTCCCTGGT 60.245 47.826 2.15 0.00 43.41 4.00
200 201 4.018779 CCTGGAAACAATAGTTCCCTGGTA 60.019 45.833 2.15 0.00 43.41 3.25
201 202 5.340027 CCTGGAAACAATAGTTCCCTGGTAT 60.340 44.000 2.15 0.00 43.41 2.73
202 203 6.147437 TGGAAACAATAGTTCCCTGGTATT 57.853 37.500 0.92 0.00 32.53 1.89
203 204 6.184789 TGGAAACAATAGTTCCCTGGTATTC 58.815 40.000 0.92 0.00 32.53 1.75
205 206 6.890268 GGAAACAATAGTTCCCTGGTATTCTT 59.110 38.462 0.00 0.00 36.84 2.52
206 207 7.067129 GGAAACAATAGTTCCCTGGTATTCTTC 59.933 40.741 0.00 0.00 36.84 2.87
210 211 8.265764 ACAATAGTTCCCTGGTATTCTTCTTAC 58.734 37.037 0.00 0.00 0.00 2.34
211 212 8.487028 CAATAGTTCCCTGGTATTCTTCTTACT 58.513 37.037 0.00 0.00 0.00 2.24
212 213 6.547930 AGTTCCCTGGTATTCTTCTTACTC 57.452 41.667 0.00 0.00 0.00 2.59
213 214 5.425862 AGTTCCCTGGTATTCTTCTTACTCC 59.574 44.000 0.00 0.00 0.00 3.85
214 215 4.296056 TCCCTGGTATTCTTCTTACTCCC 58.704 47.826 0.00 0.00 0.00 4.30
216 217 3.492829 CCTGGTATTCTTCTTACTCCCGC 60.493 52.174 0.00 0.00 0.00 6.13
217 218 2.433239 TGGTATTCTTCTTACTCCCGCC 59.567 50.000 0.00 0.00 0.00 6.13
219 220 0.179081 ATTCTTCTTACTCCCGCCGC 60.179 55.000 0.00 0.00 0.00 6.53
221 222 3.735037 CTTCTTACTCCCGCCGCCC 62.735 68.421 0.00 0.00 0.00 6.13
222 223 4.772231 TCTTACTCCCGCCGCCCT 62.772 66.667 0.00 0.00 0.00 5.19
223 224 4.530857 CTTACTCCCGCCGCCCTG 62.531 72.222 0.00 0.00 0.00 4.45
291 292 2.985116 GCCCTCCCCCAACCTCTTC 61.985 68.421 0.00 0.00 0.00 2.87
292 293 2.309504 CCCTCCCCCAACCTCTTCC 61.310 68.421 0.00 0.00 0.00 3.46
293 294 2.309504 CCTCCCCCAACCTCTTCCC 61.310 68.421 0.00 0.00 0.00 3.97
295 296 1.850755 TCCCCCAACCTCTTCCCAC 60.851 63.158 0.00 0.00 0.00 4.61
296 297 2.763902 CCCCAACCTCTTCCCACC 59.236 66.667 0.00 0.00 0.00 4.61
297 298 2.351276 CCCAACCTCTTCCCACCG 59.649 66.667 0.00 0.00 0.00 4.94
298 299 2.359975 CCAACCTCTTCCCACCGC 60.360 66.667 0.00 0.00 0.00 5.68
299 300 2.359975 CAACCTCTTCCCACCGCC 60.360 66.667 0.00 0.00 0.00 6.13
300 301 4.016706 AACCTCTTCCCACCGCCG 62.017 66.667 0.00 0.00 0.00 6.46
327 328 4.293671 CCACCGGCCCCCTCAAAA 62.294 66.667 0.00 0.00 0.00 2.44
328 329 2.203567 CACCGGCCCCCTCAAAAA 60.204 61.111 0.00 0.00 0.00 1.94
329 330 1.609210 CACCGGCCCCCTCAAAAAT 60.609 57.895 0.00 0.00 0.00 1.82
330 331 0.323908 CACCGGCCCCCTCAAAAATA 60.324 55.000 0.00 0.00 0.00 1.40
331 332 0.410270 ACCGGCCCCCTCAAAAATAA 59.590 50.000 0.00 0.00 0.00 1.40
332 333 1.203199 ACCGGCCCCCTCAAAAATAAA 60.203 47.619 0.00 0.00 0.00 1.40
333 334 1.903183 CCGGCCCCCTCAAAAATAAAA 59.097 47.619 0.00 0.00 0.00 1.52
334 335 2.303311 CCGGCCCCCTCAAAAATAAAAA 59.697 45.455 0.00 0.00 0.00 1.94
409 411 4.694339 ACATACGCTTGGGAATCTTAGAC 58.306 43.478 0.00 0.00 0.00 2.59
413 415 3.244422 ACGCTTGGGAATCTTAGACACAA 60.244 43.478 0.00 0.00 0.00 3.33
420 422 3.691609 GGAATCTTAGACACAAAGGCCTG 59.308 47.826 5.69 0.00 0.00 4.85
502 513 8.823220 AACCTTGGAGCATTACATTAAATAGT 57.177 30.769 0.00 0.00 0.00 2.12
505 516 9.778741 CCTTGGAGCATTACATTAAATAGTAGA 57.221 33.333 0.00 0.00 0.00 2.59
512 523 7.965107 GCATTACATTAAATAGTAGAGGCATGC 59.035 37.037 9.90 9.90 0.00 4.06
513 524 9.002600 CATTACATTAAATAGTAGAGGCATGCA 57.997 33.333 21.36 0.00 0.00 3.96
515 526 7.880160 ACATTAAATAGTAGAGGCATGCAAA 57.120 32.000 21.36 0.00 0.00 3.68
516 527 7.707104 ACATTAAATAGTAGAGGCATGCAAAC 58.293 34.615 21.36 11.11 0.00 2.93
527 1025 5.244626 AGAGGCATGCAAACTATTTTTCACT 59.755 36.000 21.36 1.14 0.00 3.41
622 1120 0.493639 TAGCCCTGCTATCCCATCCT 59.506 55.000 0.00 0.00 40.44 3.24
708 1207 9.598517 GAATCAAACATATTAGGCCAAATGAAA 57.401 29.630 5.01 0.00 0.00 2.69
709 1208 9.956640 AATCAAACATATTAGGCCAAATGAAAA 57.043 25.926 5.01 0.00 0.00 2.29
710 1209 9.956640 ATCAAACATATTAGGCCAAATGAAAAA 57.043 25.926 5.01 0.00 0.00 1.94
749 1253 7.556733 TTTATAGGTGTTGGCTAAATTACCG 57.443 36.000 6.53 0.00 34.65 4.02
783 1292 4.748102 TGTTGGCTAAACTACTGAAAGACG 59.252 41.667 4.78 0.00 39.70 4.18
893 1413 8.628882 AAAAAGAATTGTCCGAAAAACTAGTG 57.371 30.769 0.00 0.00 0.00 2.74
894 1414 5.941948 AGAATTGTCCGAAAAACTAGTGG 57.058 39.130 0.00 0.00 0.00 4.00
927 1447 2.203625 GGCCCACAAAAGGAGCCA 60.204 61.111 0.00 0.00 41.71 4.75
928 1448 1.610379 GGCCCACAAAAGGAGCCAT 60.610 57.895 0.00 0.00 41.71 4.40
930 1450 1.937546 GCCCACAAAAGGAGCCATCG 61.938 60.000 0.00 0.00 0.00 3.84
931 1451 0.609131 CCCACAAAAGGAGCCATCGT 60.609 55.000 0.00 0.00 0.00 3.73
932 1452 0.804989 CCACAAAAGGAGCCATCGTC 59.195 55.000 0.00 0.00 0.00 4.20
933 1453 1.611673 CCACAAAAGGAGCCATCGTCT 60.612 52.381 0.00 0.00 0.00 4.18
934 1454 2.154462 CACAAAAGGAGCCATCGTCTT 58.846 47.619 0.00 0.00 0.00 3.01
935 1455 2.095567 CACAAAAGGAGCCATCGTCTTG 60.096 50.000 0.00 0.00 0.00 3.02
938 1458 2.568623 AAGGAGCCATCGTCTTGTTT 57.431 45.000 0.00 0.00 0.00 2.83
965 4796 0.179029 CCTCTCCCTCTCTCGAGTCC 60.179 65.000 13.13 0.00 35.43 3.85
1088 4940 0.405585 CAGAACCATCCCACCACCTT 59.594 55.000 0.00 0.00 0.00 3.50
1092 4944 1.378514 CCATCCCACCACCTTTCGG 60.379 63.158 0.00 0.00 0.00 4.30
1117 5054 2.442212 TCACAGCACGGTATTTTCGA 57.558 45.000 0.00 0.00 0.00 3.71
1185 5128 2.203126 GATTCTCCCCTGCTGGCG 60.203 66.667 3.63 0.00 0.00 5.69
1286 5242 4.002316 CCTCTTCTCTTTTGCTCTTCAGG 58.998 47.826 0.00 0.00 0.00 3.86
1287 5243 4.262808 CCTCTTCTCTTTTGCTCTTCAGGA 60.263 45.833 0.00 0.00 0.00 3.86
1288 5244 4.892433 TCTTCTCTTTTGCTCTTCAGGAG 58.108 43.478 0.00 0.00 44.49 3.69
1289 5245 4.346418 TCTTCTCTTTTGCTCTTCAGGAGT 59.654 41.667 0.00 0.00 43.62 3.85
1290 5246 5.540337 TCTTCTCTTTTGCTCTTCAGGAGTA 59.460 40.000 0.00 0.00 43.62 2.59
1291 5247 6.212388 TCTTCTCTTTTGCTCTTCAGGAGTAT 59.788 38.462 0.00 0.00 43.62 2.12
1292 5248 5.971763 TCTCTTTTGCTCTTCAGGAGTATC 58.028 41.667 0.00 0.00 43.62 2.24
1293 5249 5.719085 TCTCTTTTGCTCTTCAGGAGTATCT 59.281 40.000 0.00 0.00 43.62 1.98
1294 5250 5.971763 TCTTTTGCTCTTCAGGAGTATCTC 58.028 41.667 0.00 0.00 43.62 2.75
1311 5267 1.280133 TCTCCCAGTCCAGCAATTCAG 59.720 52.381 0.00 0.00 0.00 3.02
1325 5290 1.293062 ATTCAGGGACCATCTGCACT 58.707 50.000 0.00 0.00 32.63 4.40
1393 5693 3.379688 TGTGTTTGCTTGCACATTCAGTA 59.620 39.130 0.00 0.00 40.24 2.74
1395 5695 3.243367 TGTTTGCTTGCACATTCAGTACC 60.243 43.478 0.00 0.00 0.00 3.34
1397 5697 2.153645 TGCTTGCACATTCAGTACCTG 58.846 47.619 0.00 0.00 0.00 4.00
1398 5698 1.470098 GCTTGCACATTCAGTACCTGG 59.530 52.381 0.00 0.00 31.51 4.45
1481 5841 1.378762 GTACCTGGCTGCCTGGAAA 59.621 57.895 40.53 27.87 44.09 3.13
1482 5842 0.034089 GTACCTGGCTGCCTGGAAAT 60.034 55.000 40.53 25.64 44.09 2.17
1483 5843 0.255890 TACCTGGCTGCCTGGAAATC 59.744 55.000 40.53 6.47 44.09 2.17
1484 5844 1.305623 CCTGGCTGCCTGGAAATCT 59.694 57.895 33.82 0.00 44.09 2.40
1485 5845 1.035932 CCTGGCTGCCTGGAAATCTG 61.036 60.000 33.82 9.65 44.09 2.90
1486 5846 1.000521 TGGCTGCCTGGAAATCTGG 60.001 57.895 21.03 0.00 37.51 3.86
1487 5847 1.304282 GGCTGCCTGGAAATCTGGA 59.696 57.895 12.43 0.00 36.68 3.86
1488 5848 0.323725 GGCTGCCTGGAAATCTGGAA 60.324 55.000 12.43 0.00 36.68 3.53
1504 5864 5.441718 TCTGGAATATCTGGAAGCAAAGT 57.558 39.130 0.00 0.00 0.00 2.66
1558 5926 2.116125 GAAGGGTGGGCTGCTGTT 59.884 61.111 0.00 0.00 0.00 3.16
1572 5940 4.013050 GCTGCTGTTCTTAAGGAGGATTT 58.987 43.478 1.85 0.00 33.99 2.17
1573 5941 5.186198 GCTGCTGTTCTTAAGGAGGATTTA 58.814 41.667 1.85 0.00 33.99 1.40
1739 6113 4.082125 GGGCATAATAATCCTGGGTTCAG 58.918 47.826 0.00 0.00 40.59 3.02
1896 6276 4.082125 ACGCCTCTTGGAATCTTTTTGAT 58.918 39.130 0.00 0.00 36.89 2.57
2050 6456 1.786937 ACTCATTCGGCTGAGATCCT 58.213 50.000 18.20 0.00 44.48 3.24
2248 6654 5.524535 AGGGCTCTAATCTCTCTTGTACTT 58.475 41.667 0.00 0.00 0.00 2.24
2250 6656 5.596772 GGGCTCTAATCTCTCTTGTACTTCT 59.403 44.000 0.00 0.00 0.00 2.85
2353 6759 0.323633 TGTTGGATGTGCCTGATGGG 60.324 55.000 0.00 0.00 37.63 4.00
2445 6851 1.271597 ACTTTGAGGGCAGCTAGTTGG 60.272 52.381 8.78 0.00 0.00 3.77
2446 6852 1.003580 CTTTGAGGGCAGCTAGTTGGA 59.996 52.381 8.78 0.00 0.00 3.53
2447 6853 1.289160 TTGAGGGCAGCTAGTTGGAT 58.711 50.000 8.78 0.00 0.00 3.41
2661 7082 7.781219 TGTTGGCTCAAGTGGTATAGTACTATA 59.219 37.037 17.03 17.03 0.00 1.31
2716 7137 6.966435 AGTTGATTGGTTCTTTGTTTGTTG 57.034 33.333 0.00 0.00 0.00 3.33
2726 7147 4.681744 TCTTTGTTTGTTGAAGGATGTGC 58.318 39.130 0.00 0.00 0.00 4.57
2941 7471 9.973661 TTAATCTTTACAGGGAATGAAGATCAA 57.026 29.630 0.00 0.00 33.51 2.57
3133 9121 6.543465 CACCAGGTTATTCAAATGCTCATCTA 59.457 38.462 0.00 0.00 0.00 1.98
3164 9152 6.369065 GCTATGCTTGTAACTGTCTTTAGTGT 59.631 38.462 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.865365 ACAGAAGCTGACGTTAGATAAAGC 59.135 41.667 12.13 2.34 35.18 3.51
1 2 6.952935 AACAGAAGCTGACGTTAGATAAAG 57.047 37.500 12.13 0.76 35.18 1.85
2 3 7.033791 CCTAACAGAAGCTGACGTTAGATAAA 58.966 38.462 21.94 0.00 42.11 1.40
3 4 6.152323 ACCTAACAGAAGCTGACGTTAGATAA 59.848 38.462 21.94 0.00 42.11 1.75
4 5 5.651139 ACCTAACAGAAGCTGACGTTAGATA 59.349 40.000 21.94 0.00 42.11 1.98
5 6 4.463186 ACCTAACAGAAGCTGACGTTAGAT 59.537 41.667 21.94 0.75 42.11 1.98
7 8 4.175787 ACCTAACAGAAGCTGACGTTAG 57.824 45.455 16.78 16.78 40.20 2.34
9 10 3.470645 AACCTAACAGAAGCTGACGTT 57.529 42.857 0.82 0.00 35.18 3.99
10 11 3.470645 AAACCTAACAGAAGCTGACGT 57.529 42.857 0.82 0.00 35.18 4.34
11 12 5.063564 GGATAAAACCTAACAGAAGCTGACG 59.936 44.000 0.82 0.00 35.18 4.35
12 13 5.063564 CGGATAAAACCTAACAGAAGCTGAC 59.936 44.000 0.82 0.00 35.18 3.51
13 14 5.046878 TCGGATAAAACCTAACAGAAGCTGA 60.047 40.000 0.82 0.00 35.18 4.26
14 15 5.175859 TCGGATAAAACCTAACAGAAGCTG 58.824 41.667 0.00 0.00 37.52 4.24
15 16 5.416271 TCGGATAAAACCTAACAGAAGCT 57.584 39.130 0.00 0.00 0.00 3.74
16 17 5.050972 CGATCGGATAAAACCTAACAGAAGC 60.051 44.000 7.38 0.00 0.00 3.86
18 19 5.353938 CCGATCGGATAAAACCTAACAGAA 58.646 41.667 30.62 0.00 37.50 3.02
19 20 4.202182 CCCGATCGGATAAAACCTAACAGA 60.202 45.833 35.42 0.00 37.50 3.41
20 21 4.056050 CCCGATCGGATAAAACCTAACAG 58.944 47.826 35.42 9.28 37.50 3.16
21 22 3.451902 ACCCGATCGGATAAAACCTAACA 59.548 43.478 35.42 0.00 37.50 2.41
22 23 4.063998 ACCCGATCGGATAAAACCTAAC 57.936 45.455 35.42 0.00 37.50 2.34
23 24 4.444536 CAACCCGATCGGATAAAACCTAA 58.555 43.478 35.42 0.00 37.50 2.69
24 25 3.742013 GCAACCCGATCGGATAAAACCTA 60.742 47.826 35.42 0.00 37.50 3.08
25 26 2.914059 CAACCCGATCGGATAAAACCT 58.086 47.619 35.42 0.00 37.50 3.50
26 27 1.332686 GCAACCCGATCGGATAAAACC 59.667 52.381 35.42 12.30 37.50 3.27
27 28 2.011222 TGCAACCCGATCGGATAAAAC 58.989 47.619 35.42 18.37 37.50 2.43
31 32 1.066752 CGTGCAACCCGATCGGATA 59.933 57.895 35.42 13.10 37.50 2.59
33 34 3.687102 ACGTGCAACCCGATCGGA 61.687 61.111 35.42 12.46 37.50 4.55
34 35 3.487202 CACGTGCAACCCGATCGG 61.487 66.667 27.65 27.65 37.81 4.18
35 36 1.009903 TAACACGTGCAACCCGATCG 61.010 55.000 17.22 8.51 0.00 3.69
36 37 1.149987 TTAACACGTGCAACCCGATC 58.850 50.000 17.22 0.00 0.00 3.69
37 38 1.595466 TTTAACACGTGCAACCCGAT 58.405 45.000 17.22 0.00 0.00 4.18
38 39 1.376543 TTTTAACACGTGCAACCCGA 58.623 45.000 17.22 0.00 0.00 5.14
39 40 2.190325 TTTTTAACACGTGCAACCCG 57.810 45.000 17.22 0.00 0.00 5.28
41 42 4.623595 CCCATATTTTTAACACGTGCAACC 59.376 41.667 17.22 0.00 0.00 3.77
42 43 4.623595 CCCCATATTTTTAACACGTGCAAC 59.376 41.667 17.22 0.00 0.00 4.17
43 44 4.523173 TCCCCATATTTTTAACACGTGCAA 59.477 37.500 17.22 7.32 0.00 4.08
44 45 4.079970 TCCCCATATTTTTAACACGTGCA 58.920 39.130 17.22 0.00 0.00 4.57
45 46 4.705337 TCCCCATATTTTTAACACGTGC 57.295 40.909 17.22 0.00 0.00 5.34
46 47 5.040635 GCATCCCCATATTTTTAACACGTG 58.959 41.667 15.48 15.48 0.00 4.49
47 48 4.953579 AGCATCCCCATATTTTTAACACGT 59.046 37.500 0.00 0.00 0.00 4.49
48 49 5.514274 AGCATCCCCATATTTTTAACACG 57.486 39.130 0.00 0.00 0.00 4.49
49 50 7.286775 TCCTAAGCATCCCCATATTTTTAACAC 59.713 37.037 0.00 0.00 0.00 3.32
50 51 7.358263 TCCTAAGCATCCCCATATTTTTAACA 58.642 34.615 0.00 0.00 0.00 2.41
51 52 7.039714 CCTCCTAAGCATCCCCATATTTTTAAC 60.040 40.741 0.00 0.00 0.00 2.01
53 54 6.552008 CCTCCTAAGCATCCCCATATTTTTA 58.448 40.000 0.00 0.00 0.00 1.52
55 56 4.754160 GCCTCCTAAGCATCCCCATATTTT 60.754 45.833 0.00 0.00 0.00 1.82
56 57 3.245407 GCCTCCTAAGCATCCCCATATTT 60.245 47.826 0.00 0.00 0.00 1.40
58 59 1.918957 GCCTCCTAAGCATCCCCATAT 59.081 52.381 0.00 0.00 0.00 1.78
59 60 1.362224 GCCTCCTAAGCATCCCCATA 58.638 55.000 0.00 0.00 0.00 2.74
61 62 1.307778 TGCCTCCTAAGCATCCCCA 60.308 57.895 0.00 0.00 34.69 4.96
62 63 1.056700 TCTGCCTCCTAAGCATCCCC 61.057 60.000 0.00 0.00 40.04 4.81
63 64 0.107643 GTCTGCCTCCTAAGCATCCC 59.892 60.000 0.00 0.00 40.04 3.85
66 67 1.418334 ATCGTCTGCCTCCTAAGCAT 58.582 50.000 0.00 0.00 40.04 3.79
67 68 1.134699 CAATCGTCTGCCTCCTAAGCA 60.135 52.381 0.00 0.00 38.82 3.91
68 69 1.137086 TCAATCGTCTGCCTCCTAAGC 59.863 52.381 0.00 0.00 0.00 3.09
69 70 3.526931 TTCAATCGTCTGCCTCCTAAG 57.473 47.619 0.00 0.00 0.00 2.18
70 71 3.973206 TTTCAATCGTCTGCCTCCTAA 57.027 42.857 0.00 0.00 0.00 2.69
71 72 4.487714 AATTTCAATCGTCTGCCTCCTA 57.512 40.909 0.00 0.00 0.00 2.94
73 74 3.485877 CGAAATTTCAATCGTCTGCCTCC 60.486 47.826 17.99 0.00 34.48 4.30
74 75 3.674423 CGAAATTTCAATCGTCTGCCTC 58.326 45.455 17.99 0.00 34.48 4.70
75 76 3.747099 CGAAATTTCAATCGTCTGCCT 57.253 42.857 17.99 0.00 34.48 4.75
83 84 6.604930 TCCGACCTAAAACGAAATTTCAATC 58.395 36.000 17.99 2.89 0.00 2.67
86 87 5.299148 TCTCCGACCTAAAACGAAATTTCA 58.701 37.500 17.99 0.00 0.00 2.69
87 88 5.851047 TCTCCGACCTAAAACGAAATTTC 57.149 39.130 8.20 8.20 0.00 2.17
88 89 6.428771 TGATTCTCCGACCTAAAACGAAATTT 59.571 34.615 0.00 0.00 0.00 1.82
90 91 5.484715 TGATTCTCCGACCTAAAACGAAAT 58.515 37.500 0.00 0.00 0.00 2.17
91 92 4.885413 TGATTCTCCGACCTAAAACGAAA 58.115 39.130 0.00 0.00 0.00 3.46
92 93 4.524316 TGATTCTCCGACCTAAAACGAA 57.476 40.909 0.00 0.00 0.00 3.85
93 94 4.240096 GTTGATTCTCCGACCTAAAACGA 58.760 43.478 0.00 0.00 0.00 3.85
94 95 3.991773 TGTTGATTCTCCGACCTAAAACG 59.008 43.478 0.00 0.00 0.00 3.60
96 97 5.800296 TCATGTTGATTCTCCGACCTAAAA 58.200 37.500 0.00 0.00 0.00 1.52
98 99 5.414789 TTCATGTTGATTCTCCGACCTAA 57.585 39.130 0.00 0.00 0.00 2.69
100 101 3.866651 CTTCATGTTGATTCTCCGACCT 58.133 45.455 0.00 0.00 0.00 3.85
101 102 2.352960 GCTTCATGTTGATTCTCCGACC 59.647 50.000 0.00 0.00 0.00 4.79
102 103 2.029728 CGCTTCATGTTGATTCTCCGAC 59.970 50.000 0.00 0.00 0.00 4.79
103 104 2.270923 CGCTTCATGTTGATTCTCCGA 58.729 47.619 0.00 0.00 0.00 4.55
104 105 2.002586 ACGCTTCATGTTGATTCTCCG 58.997 47.619 0.00 0.00 0.00 4.63
105 106 4.870426 TCTAACGCTTCATGTTGATTCTCC 59.130 41.667 0.00 0.00 0.00 3.71
106 107 6.595772 ATCTAACGCTTCATGTTGATTCTC 57.404 37.500 0.00 0.00 0.00 2.87
107 108 8.492673 TTTATCTAACGCTTCATGTTGATTCT 57.507 30.769 0.00 0.00 0.00 2.40
134 135 3.117888 AGAGATTATCCGGTGCATTGGTT 60.118 43.478 0.00 2.22 0.00 3.67
135 136 2.439507 AGAGATTATCCGGTGCATTGGT 59.560 45.455 0.00 0.00 0.00 3.67
136 137 3.131709 AGAGATTATCCGGTGCATTGG 57.868 47.619 0.00 0.00 0.00 3.16
137 138 4.384056 AGAAGAGATTATCCGGTGCATTG 58.616 43.478 0.00 0.00 0.00 2.82
138 139 4.696479 AGAAGAGATTATCCGGTGCATT 57.304 40.909 0.00 0.00 0.00 3.56
140 141 3.321111 GGTAGAAGAGATTATCCGGTGCA 59.679 47.826 0.00 0.00 0.00 4.57
141 142 3.574826 AGGTAGAAGAGATTATCCGGTGC 59.425 47.826 0.00 0.00 0.00 5.01
142 143 4.083217 CGAGGTAGAAGAGATTATCCGGTG 60.083 50.000 0.00 0.00 0.00 4.94
143 144 4.073549 CGAGGTAGAAGAGATTATCCGGT 58.926 47.826 0.00 0.00 0.00 5.28
144 145 4.325119 TCGAGGTAGAAGAGATTATCCGG 58.675 47.826 0.00 0.00 0.00 5.14
145 146 5.943706 TTCGAGGTAGAAGAGATTATCCG 57.056 43.478 0.00 0.00 0.00 4.18
146 147 7.662897 ACAATTCGAGGTAGAAGAGATTATCC 58.337 38.462 0.00 0.00 33.19 2.59
147 148 9.535878 AAACAATTCGAGGTAGAAGAGATTATC 57.464 33.333 0.00 0.00 33.19 1.75
148 149 9.319143 CAAACAATTCGAGGTAGAAGAGATTAT 57.681 33.333 0.00 0.00 33.19 1.28
149 150 8.311836 ACAAACAATTCGAGGTAGAAGAGATTA 58.688 33.333 0.00 0.00 33.19 1.75
150 151 7.162082 ACAAACAATTCGAGGTAGAAGAGATT 58.838 34.615 0.00 0.00 33.19 2.40
151 152 6.702329 ACAAACAATTCGAGGTAGAAGAGAT 58.298 36.000 0.00 0.00 33.19 2.75
152 153 6.097915 ACAAACAATTCGAGGTAGAAGAGA 57.902 37.500 0.00 0.00 33.19 3.10
153 154 6.128526 GGAACAAACAATTCGAGGTAGAAGAG 60.129 42.308 0.00 0.00 33.19 2.85
154 155 5.699458 GGAACAAACAATTCGAGGTAGAAGA 59.301 40.000 0.00 0.00 33.19 2.87
155 156 5.701290 AGGAACAAACAATTCGAGGTAGAAG 59.299 40.000 0.00 0.00 33.19 2.85
156 157 5.468746 CAGGAACAAACAATTCGAGGTAGAA 59.531 40.000 0.00 0.00 34.31 2.10
158 159 4.154195 CCAGGAACAAACAATTCGAGGTAG 59.846 45.833 0.00 0.00 0.00 3.18
159 160 4.069304 CCAGGAACAAACAATTCGAGGTA 58.931 43.478 0.00 0.00 0.00 3.08
162 163 4.829064 TTCCAGGAACAAACAATTCGAG 57.171 40.909 0.00 0.00 0.00 4.04
163 164 4.399618 TGTTTCCAGGAACAAACAATTCGA 59.600 37.500 0.00 0.00 39.10 3.71
164 165 4.677584 TGTTTCCAGGAACAAACAATTCG 58.322 39.130 0.00 0.00 39.10 3.34
181 182 7.829706 AGAAGAATACCAGGGAACTATTGTTTC 59.170 37.037 0.00 0.00 40.21 2.78
182 183 7.699878 AGAAGAATACCAGGGAACTATTGTTT 58.300 34.615 0.00 0.00 40.21 2.83
183 184 7.272144 AGAAGAATACCAGGGAACTATTGTT 57.728 36.000 0.00 0.00 40.21 2.83
184 185 6.893020 AGAAGAATACCAGGGAACTATTGT 57.107 37.500 0.00 0.00 40.21 2.71
188 189 6.610425 GGAGTAAGAAGAATACCAGGGAACTA 59.390 42.308 0.00 0.00 40.21 2.24
189 190 5.425862 GGAGTAAGAAGAATACCAGGGAACT 59.574 44.000 0.00 0.00 46.44 3.01
191 192 4.720273 GGGAGTAAGAAGAATACCAGGGAA 59.280 45.833 0.00 0.00 0.00 3.97
192 193 4.296056 GGGAGTAAGAAGAATACCAGGGA 58.704 47.826 0.00 0.00 0.00 4.20
193 194 3.069729 CGGGAGTAAGAAGAATACCAGGG 59.930 52.174 0.00 0.00 0.00 4.45
194 195 3.492829 GCGGGAGTAAGAAGAATACCAGG 60.493 52.174 0.00 0.00 0.00 4.45
195 196 3.492829 GGCGGGAGTAAGAAGAATACCAG 60.493 52.174 0.00 0.00 0.00 4.00
196 197 2.433239 GGCGGGAGTAAGAAGAATACCA 59.567 50.000 0.00 0.00 0.00 3.25
197 198 2.545322 CGGCGGGAGTAAGAAGAATACC 60.545 54.545 0.00 0.00 0.00 2.73
198 199 2.740452 CGGCGGGAGTAAGAAGAATAC 58.260 52.381 0.00 0.00 0.00 1.89
199 200 1.068127 GCGGCGGGAGTAAGAAGAATA 59.932 52.381 9.78 0.00 0.00 1.75
200 201 0.179081 GCGGCGGGAGTAAGAAGAAT 60.179 55.000 9.78 0.00 0.00 2.40
201 202 1.217244 GCGGCGGGAGTAAGAAGAA 59.783 57.895 9.78 0.00 0.00 2.52
202 203 2.718073 GGCGGCGGGAGTAAGAAGA 61.718 63.158 9.78 0.00 0.00 2.87
203 204 2.202892 GGCGGCGGGAGTAAGAAG 60.203 66.667 9.78 0.00 0.00 2.85
205 206 4.772231 AGGGCGGCGGGAGTAAGA 62.772 66.667 9.78 0.00 0.00 2.10
206 207 4.530857 CAGGGCGGCGGGAGTAAG 62.531 72.222 9.78 0.00 0.00 2.34
273 274 2.941583 AAGAGGTTGGGGGAGGGC 60.942 66.667 0.00 0.00 0.00 5.19
274 275 2.309504 GGAAGAGGTTGGGGGAGGG 61.310 68.421 0.00 0.00 0.00 4.30
275 276 2.309504 GGGAAGAGGTTGGGGGAGG 61.310 68.421 0.00 0.00 0.00 4.30
277 278 1.850755 GTGGGAAGAGGTTGGGGGA 60.851 63.158 0.00 0.00 0.00 4.81
278 279 2.763902 GTGGGAAGAGGTTGGGGG 59.236 66.667 0.00 0.00 0.00 5.40
279 280 2.763902 GGTGGGAAGAGGTTGGGG 59.236 66.667 0.00 0.00 0.00 4.96
280 281 2.351276 CGGTGGGAAGAGGTTGGG 59.649 66.667 0.00 0.00 0.00 4.12
281 282 2.359975 GCGGTGGGAAGAGGTTGG 60.360 66.667 0.00 0.00 0.00 3.77
283 284 4.016706 CGGCGGTGGGAAGAGGTT 62.017 66.667 0.00 0.00 0.00 3.50
310 311 3.700015 TATTTTTGAGGGGGCCGGTGG 62.700 57.143 1.90 0.00 0.00 4.61
311 312 0.323908 TATTTTTGAGGGGGCCGGTG 60.324 55.000 1.90 0.00 0.00 4.94
312 313 0.410270 TTATTTTTGAGGGGGCCGGT 59.590 50.000 1.90 0.00 0.00 5.28
313 314 1.562783 TTTATTTTTGAGGGGGCCGG 58.437 50.000 0.00 0.00 0.00 6.13
314 315 3.007506 ACTTTTTATTTTTGAGGGGGCCG 59.992 43.478 0.00 0.00 0.00 6.13
315 316 4.634012 ACTTTTTATTTTTGAGGGGGCC 57.366 40.909 0.00 0.00 0.00 5.80
316 317 7.119116 CACATAACTTTTTATTTTTGAGGGGGC 59.881 37.037 0.00 0.00 0.00 5.80
317 318 8.154203 ACACATAACTTTTTATTTTTGAGGGGG 58.846 33.333 0.00 0.00 0.00 5.40
318 319 8.987890 CACACATAACTTTTTATTTTTGAGGGG 58.012 33.333 0.00 0.00 0.00 4.79
319 320 8.987890 CCACACATAACTTTTTATTTTTGAGGG 58.012 33.333 0.00 0.00 0.00 4.30
320 321 9.541143 ACCACACATAACTTTTTATTTTTGAGG 57.459 29.630 0.00 0.00 0.00 3.86
328 329 9.912634 CTCATTTGACCACACATAACTTTTTAT 57.087 29.630 0.00 0.00 0.00 1.40
329 330 7.865385 GCTCATTTGACCACACATAACTTTTTA 59.135 33.333 0.00 0.00 0.00 1.52
330 331 6.701400 GCTCATTTGACCACACATAACTTTTT 59.299 34.615 0.00 0.00 0.00 1.94
331 332 6.183360 TGCTCATTTGACCACACATAACTTTT 60.183 34.615 0.00 0.00 0.00 2.27
332 333 5.301551 TGCTCATTTGACCACACATAACTTT 59.698 36.000 0.00 0.00 0.00 2.66
333 334 4.826733 TGCTCATTTGACCACACATAACTT 59.173 37.500 0.00 0.00 0.00 2.66
334 335 4.397420 TGCTCATTTGACCACACATAACT 58.603 39.130 0.00 0.00 0.00 2.24
409 411 3.415212 TCTCTGATTTCAGGCCTTTGTG 58.585 45.455 0.00 0.00 43.91 3.33
413 415 6.461640 CAAAATTTCTCTGATTTCAGGCCTT 58.538 36.000 0.00 0.00 43.91 4.35
420 422 9.351570 GTGATCTTCCAAAATTTCTCTGATTTC 57.648 33.333 0.00 0.00 0.00 2.17
502 513 6.434028 AGTGAAAAATAGTTTGCATGCCTCTA 59.566 34.615 16.68 14.53 34.66 2.43
505 516 5.473066 AGTGAAAAATAGTTTGCATGCCT 57.527 34.783 16.68 7.75 34.66 4.75
561 1059 7.026631 TCTGACCTGTTTGTAGTCATTTTTG 57.973 36.000 0.00 0.00 39.64 2.44
622 1120 1.066430 CGATTCCTTCGGTCTTTCCCA 60.066 52.381 0.00 0.00 44.28 4.37
723 1227 9.275398 CGGTAATTTAGCCAACACCTATAAATA 57.725 33.333 0.26 0.00 0.00 1.40
749 1253 4.342951 AGTTTAGCCAACAACCCCTAAAAC 59.657 41.667 0.00 0.00 37.93 2.43
783 1292 8.135529 AGCTACCAGTTTTTGTAGAAATGTTTC 58.864 33.333 0.00 0.00 37.26 2.78
873 1393 5.684550 ACCACTAGTTTTTCGGACAATTC 57.315 39.130 3.32 0.00 0.00 2.17
889 1409 4.223953 CCTTCTATAGGCCTCAACCACTA 58.776 47.826 9.68 0.00 37.17 2.74
890 1410 3.041946 CCTTCTATAGGCCTCAACCACT 58.958 50.000 9.68 0.00 37.17 4.00
938 1458 3.006967 CGAGAGAGGGAGAGGAAACAAAA 59.993 47.826 0.00 0.00 0.00 2.44
990 4821 2.537560 CGCCGCCATGGAGATGAAC 61.538 63.158 18.40 0.00 40.56 3.18
1117 5054 0.609131 CGATGGGAGCAAACAAGGGT 60.609 55.000 0.00 0.00 0.00 4.34
1185 5128 1.207593 GCGTCACCAGCATTCACAC 59.792 57.895 0.00 0.00 34.19 3.82
1286 5242 1.781786 TGCTGGACTGGGAGATACTC 58.218 55.000 0.00 0.00 0.00 2.59
1287 5243 2.254152 TTGCTGGACTGGGAGATACT 57.746 50.000 0.00 0.00 0.00 2.12
1288 5244 3.118261 TGAATTGCTGGACTGGGAGATAC 60.118 47.826 0.00 0.00 0.00 2.24
1289 5245 3.114606 TGAATTGCTGGACTGGGAGATA 58.885 45.455 0.00 0.00 0.00 1.98
1290 5246 1.918262 TGAATTGCTGGACTGGGAGAT 59.082 47.619 0.00 0.00 0.00 2.75
1291 5247 1.280133 CTGAATTGCTGGACTGGGAGA 59.720 52.381 0.00 0.00 0.00 3.71
1292 5248 1.681166 CCTGAATTGCTGGACTGGGAG 60.681 57.143 0.00 0.00 37.79 4.30
1293 5249 0.329261 CCTGAATTGCTGGACTGGGA 59.671 55.000 0.00 0.00 37.79 4.37
1294 5250 0.682209 CCCTGAATTGCTGGACTGGG 60.682 60.000 0.00 0.00 37.79 4.45
1295 5251 0.329261 TCCCTGAATTGCTGGACTGG 59.671 55.000 0.00 0.00 37.79 4.00
1296 5252 1.457346 GTCCCTGAATTGCTGGACTG 58.543 55.000 8.81 0.00 43.16 3.51
1297 5253 0.329596 GGTCCCTGAATTGCTGGACT 59.670 55.000 13.61 0.00 45.29 3.85
1298 5254 0.038166 TGGTCCCTGAATTGCTGGAC 59.962 55.000 7.89 7.89 45.25 4.02
1311 5267 2.027192 TGAAAGTAGTGCAGATGGTCCC 60.027 50.000 0.00 0.00 0.00 4.46
1325 5290 3.995636 AGGATAGAGGCTGGTGAAAGTA 58.004 45.455 0.00 0.00 0.00 2.24
1393 5693 1.129917 CCTCATCATCTCAGCCAGGT 58.870 55.000 0.00 0.00 0.00 4.00
1395 5695 0.759959 AGCCTCATCATCTCAGCCAG 59.240 55.000 0.00 0.00 0.00 4.85
1397 5697 0.757512 TCAGCCTCATCATCTCAGCC 59.242 55.000 0.00 0.00 0.00 4.85
1398 5698 1.874739 GCTCAGCCTCATCATCTCAGC 60.875 57.143 0.00 0.00 0.00 4.26
1481 5841 6.011122 ACTTTGCTTCCAGATATTCCAGAT 57.989 37.500 0.00 0.00 0.00 2.90
1482 5842 5.441718 ACTTTGCTTCCAGATATTCCAGA 57.558 39.130 0.00 0.00 0.00 3.86
1483 5843 6.825721 AGTTACTTTGCTTCCAGATATTCCAG 59.174 38.462 0.00 0.00 0.00 3.86
1484 5844 6.599244 CAGTTACTTTGCTTCCAGATATTCCA 59.401 38.462 0.00 0.00 0.00 3.53
1485 5845 6.038714 CCAGTTACTTTGCTTCCAGATATTCC 59.961 42.308 0.00 0.00 0.00 3.01
1486 5846 6.823689 TCCAGTTACTTTGCTTCCAGATATTC 59.176 38.462 0.00 0.00 0.00 1.75
1487 5847 6.721318 TCCAGTTACTTTGCTTCCAGATATT 58.279 36.000 0.00 0.00 0.00 1.28
1488 5848 6.313519 TCCAGTTACTTTGCTTCCAGATAT 57.686 37.500 0.00 0.00 0.00 1.63
1504 5864 6.939730 TCACAGCATCAAAGTATTTCCAGTTA 59.060 34.615 0.00 0.00 35.03 2.24
1524 5884 3.369892 CCCTTCCAATGTAGGAGTCACAG 60.370 52.174 0.83 0.00 39.25 3.66
1572 5940 9.886132 GAGACCCTGAACTTAAGTTGATTTATA 57.114 33.333 25.17 2.62 38.56 0.98
1573 5941 7.829706 GGAGACCCTGAACTTAAGTTGATTTAT 59.170 37.037 25.17 6.47 38.56 1.40
1603 5975 8.616799 AAAGAGGTTAGGAAGTCAGATAGATT 57.383 34.615 0.00 0.00 0.00 2.40
1739 6113 4.440103 CAGCAGCATATCAAGCGAATTTTC 59.560 41.667 0.00 0.00 37.01 2.29
1896 6276 3.673902 TGCTTTATGACAGCAGTAGCAA 58.326 40.909 1.58 0.00 42.49 3.91
2027 6433 0.321346 TCTCAGCCGAATGAGTTGCA 59.679 50.000 14.14 0.00 45.70 4.08
2050 6456 0.322975 GAGCTCCTCTTTGACCTGCA 59.677 55.000 0.87 0.00 0.00 4.41
2248 6654 0.387202 GATAGAAGCGCCTGCAGAGA 59.613 55.000 17.39 0.00 46.23 3.10
2250 6656 1.066422 CGATAGAAGCGCCTGCAGA 59.934 57.895 17.39 0.00 41.53 4.26
2353 6759 2.235898 AGCTGGTGTCATCTCCTTCTTC 59.764 50.000 0.00 0.00 0.00 2.87
2445 6851 4.589374 AGTGCTGGGGTTAGTCACTATATC 59.411 45.833 0.00 0.00 35.11 1.63
2446 6852 4.557705 AGTGCTGGGGTTAGTCACTATAT 58.442 43.478 0.00 0.00 35.11 0.86
2447 6853 3.990369 AGTGCTGGGGTTAGTCACTATA 58.010 45.455 0.00 0.00 35.11 1.31
2716 7137 1.396301 CAAAGAGCTCGCACATCCTTC 59.604 52.381 8.37 0.00 0.00 3.46
2925 7455 4.841422 ACACTCTTGATCTTCATTCCCTG 58.159 43.478 0.00 0.00 0.00 4.45
2941 7471 2.038952 TGCAGGCATCTTGTAACACTCT 59.961 45.455 0.00 0.00 0.00 3.24
3164 9152 2.583024 TGCAACACCATTGGAGATGA 57.417 45.000 10.37 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.