Multiple sequence alignment - TraesCS5B01G068200

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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 TraesCS5B01G068200 chr5B 100.000 2567 0 0 1 2567 77707701 77710267 0.000000e+00 4741.0
1 TraesCS5B01G068200 chr5B 84.906 106 12 3 1938 2041 418915989 418916092 1.260000e-18 104.0
2 TraesCS5B01G068200 chr5D 88.394 2154 135 46 457 2567 74468112 74466031 0.000000e+00 2486.0
3 TraesCS5B01G068200 chr5D 75.610 533 72 38 1558 2043 510939064 510939585 7.200000e-51 211.0
4 TraesCS5B01G068200 chr5D 87.079 178 17 6 264 439 74468389 74468216 2.010000e-46 196.0
5 TraesCS5B01G068200 chr5D 74.519 416 78 22 1645 2041 354521743 354522149 3.420000e-34 156.0
6 TraesCS5B01G068200 chr5A 87.867 1022 66 21 455 1452 69868614 69867627 0.000000e+00 1147.0
7 TraesCS5B01G068200 chr5A 92.500 40 3 0 1935 1974 229516654 229516693 9.920000e-05 58.4
8 TraesCS5B01G068200 chr7B 98.537 205 2 1 2 206 175188619 175188416 6.750000e-96 361.0
9 TraesCS5B01G068200 chr7B 97.585 207 4 1 1 207 530592017 530592222 1.130000e-93 353.0
10 TraesCS5B01G068200 chr1B 98.049 205 3 1 2 206 14550416 14550619 3.140000e-94 355.0
11 TraesCS5B01G068200 chr1B 97.129 209 5 1 1 209 125321693 125321900 4.060000e-93 351.0
12 TraesCS5B01G068200 chr1B 97.573 206 4 1 1 206 593206851 593207055 4.060000e-93 351.0
13 TraesCS5B01G068200 chr1B 85.455 55 8 0 1936 1990 512732815 512732761 9.920000e-05 58.4
14 TraesCS5B01G068200 chr3B 98.039 204 2 2 3 206 828669172 828669373 1.130000e-93 353.0
15 TraesCS5B01G068200 chr3B 92.500 40 3 0 1935 1974 428134589 428134628 9.920000e-05 58.4
16 TraesCS5B01G068200 chrUn 97.573 206 4 1 1 206 67918329 67918125 4.060000e-93 351.0
17 TraesCS5B01G068200 chr6B 97.549 204 3 2 3 206 140674011 140674212 5.260000e-92 348.0
18 TraesCS5B01G068200 chr6B 96.209 211 7 1 4 214 688775689 688775898 6.800000e-91 344.0
19 TraesCS5B01G068200 chr2D 80.788 406 53 15 1592 1979 58876480 58876878 6.950000e-76 294.0
20 TraesCS5B01G068200 chr4D 77.570 107 23 1 1937 2043 509432881 509432776 2.130000e-06 63.9
21 TraesCS5B01G068200 chr7A 86.792 53 7 0 1935 1987 385325963 385325911 2.760000e-05 60.2


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 TraesCS5B01G068200 chr5B 77707701 77710267 2566 False 4741 4741 100.0000 1 2567 1 chr5B.!!$F1 2566
1 TraesCS5B01G068200 chr5D 74466031 74468389 2358 True 1341 2486 87.7365 264 2567 2 chr5D.!!$R1 2303
2 TraesCS5B01G068200 chr5D 510939064 510939585 521 False 211 211 75.6100 1558 2043 1 chr5D.!!$F2 485
3 TraesCS5B01G068200 chr5A 69867627 69868614 987 True 1147 1147 87.8670 455 1452 1 chr5A.!!$R1 997

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
22 23 0.034863 ATTGTTACGCAATCCCGGGT 60.035 50.0 22.86 4.84 43.86 5.28 F
1014 1129 0.101759 GCTCCATCGCATTTGCACAT 59.898 50.0 3.13 0.00 42.21 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1235 1352 0.692476 CTCCCATCTGGTGTTGGTGA 59.308 55.0 0.0 0.0 32.53 4.02 R
2308 2475 0.693049 TTGCCCTGTCTCTCCTTTCC 59.307 55.0 0.0 0.0 0.00 3.13 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.187351 CCAATTGTTACGCAATCCCG 57.813 50.000 4.43 0.00 46.29 5.14
20 21 1.202245 CCAATTGTTACGCAATCCCGG 60.202 52.381 4.43 0.00 46.29 5.73
21 22 1.099689 AATTGTTACGCAATCCCGGG 58.900 50.000 16.85 16.85 46.29 5.73
22 23 0.034863 ATTGTTACGCAATCCCGGGT 60.035 50.000 22.86 4.84 43.86 5.28
23 24 0.674269 TTGTTACGCAATCCCGGGTC 60.674 55.000 22.86 7.55 33.58 4.46
24 25 1.816679 GTTACGCAATCCCGGGTCC 60.817 63.158 22.86 6.38 33.58 4.46
25 26 3.374012 TTACGCAATCCCGGGTCCG 62.374 63.158 22.86 19.95 39.44 4.79
28 29 3.857038 GCAATCCCGGGTCCGCTA 61.857 66.667 22.86 0.00 38.24 4.26
29 30 3.148084 CAATCCCGGGTCCGCTAT 58.852 61.111 22.86 1.44 38.24 2.97
30 31 1.004918 CAATCCCGGGTCCGCTATC 60.005 63.158 22.86 0.00 38.24 2.08
31 32 1.458777 AATCCCGGGTCCGCTATCA 60.459 57.895 22.86 0.00 38.24 2.15
32 33 1.755393 AATCCCGGGTCCGCTATCAC 61.755 60.000 22.86 0.00 38.24 3.06
33 34 3.925090 CCCGGGTCCGCTATCACC 61.925 72.222 14.18 0.00 38.24 4.02
34 35 3.151710 CCGGGTCCGCTATCACCA 61.152 66.667 3.52 0.00 38.24 4.17
35 36 2.417516 CGGGTCCGCTATCACCAG 59.582 66.667 0.00 0.00 33.91 4.00
36 37 2.109181 GGGTCCGCTATCACCAGC 59.891 66.667 0.00 0.00 38.23 4.85
43 44 2.006772 GCTATCACCAGCGTTTCCG 58.993 57.895 0.00 0.00 37.07 4.30
44 45 0.459585 GCTATCACCAGCGTTTCCGA 60.460 55.000 0.00 0.00 35.63 4.55
45 46 1.278238 CTATCACCAGCGTTTCCGAC 58.722 55.000 0.00 0.00 35.63 4.79
46 47 0.108520 TATCACCAGCGTTTCCGACC 60.109 55.000 0.00 0.00 35.63 4.79
47 48 2.798148 ATCACCAGCGTTTCCGACCC 62.798 60.000 0.00 0.00 35.63 4.46
48 49 3.552384 ACCAGCGTTTCCGACCCA 61.552 61.111 0.00 0.00 35.63 4.51
49 50 3.047877 CCAGCGTTTCCGACCCAC 61.048 66.667 0.00 0.00 35.63 4.61
50 51 2.280524 CAGCGTTTCCGACCCACA 60.281 61.111 0.00 0.00 35.63 4.17
51 52 1.671054 CAGCGTTTCCGACCCACAT 60.671 57.895 0.00 0.00 35.63 3.21
52 53 1.671054 AGCGTTTCCGACCCACATG 60.671 57.895 0.00 0.00 35.63 3.21
53 54 2.867472 CGTTTCCGACCCACATGC 59.133 61.111 0.00 0.00 35.63 4.06
54 55 2.867472 GTTTCCGACCCACATGCG 59.133 61.111 0.00 0.00 0.00 4.73
55 56 1.964373 GTTTCCGACCCACATGCGT 60.964 57.895 0.00 0.00 0.00 5.24
56 57 1.669760 TTTCCGACCCACATGCGTC 60.670 57.895 0.00 0.00 0.00 5.19
57 58 2.384653 TTTCCGACCCACATGCGTCA 62.385 55.000 8.41 0.00 0.00 4.35
58 59 2.358125 CCGACCCACATGCGTCAA 60.358 61.111 8.41 0.00 0.00 3.18
59 60 2.677003 CCGACCCACATGCGTCAAC 61.677 63.158 8.41 0.00 0.00 3.18
60 61 2.677003 CGACCCACATGCGTCAACC 61.677 63.158 8.41 0.00 0.00 3.77
61 62 1.599518 GACCCACATGCGTCAACCA 60.600 57.895 0.00 0.00 0.00 3.67
62 63 1.577328 GACCCACATGCGTCAACCAG 61.577 60.000 0.00 0.00 0.00 4.00
63 64 2.334946 CCCACATGCGTCAACCAGG 61.335 63.158 0.00 0.00 0.00 4.45
64 65 2.562912 CACATGCGTCAACCAGGC 59.437 61.111 0.00 0.00 36.35 4.85
65 66 2.672996 ACATGCGTCAACCAGGCC 60.673 61.111 0.00 0.00 34.78 5.19
66 67 3.443045 CATGCGTCAACCAGGCCC 61.443 66.667 0.00 0.00 34.78 5.80
67 68 3.965258 ATGCGTCAACCAGGCCCA 61.965 61.111 0.00 0.00 34.78 5.36
68 69 3.505790 ATGCGTCAACCAGGCCCAA 62.506 57.895 0.00 0.00 34.78 4.12
69 70 3.670377 GCGTCAACCAGGCCCAAC 61.670 66.667 0.00 0.00 0.00 3.77
70 71 2.983592 CGTCAACCAGGCCCAACC 60.984 66.667 0.00 0.00 39.61 3.77
71 72 2.983592 GTCAACCAGGCCCAACCG 60.984 66.667 0.00 0.00 46.52 4.44
72 73 4.278513 TCAACCAGGCCCAACCGG 62.279 66.667 0.00 0.00 46.52 5.28
73 74 4.278513 CAACCAGGCCCAACCGGA 62.279 66.667 9.46 0.00 46.52 5.14
74 75 3.966543 AACCAGGCCCAACCGGAG 61.967 66.667 9.46 0.00 46.52 4.63
75 76 4.974438 ACCAGGCCCAACCGGAGA 62.974 66.667 9.46 0.00 46.52 3.71
76 77 4.101448 CCAGGCCCAACCGGAGAG 62.101 72.222 9.46 0.00 46.52 3.20
77 78 4.785453 CAGGCCCAACCGGAGAGC 62.785 72.222 9.46 5.06 46.52 4.09
79 80 4.344865 GGCCCAACCGGAGAGCAA 62.345 66.667 9.46 0.00 0.00 3.91
80 81 3.056328 GCCCAACCGGAGAGCAAC 61.056 66.667 9.46 0.00 0.00 4.17
81 82 2.429930 CCCAACCGGAGAGCAACA 59.570 61.111 9.46 0.00 0.00 3.33
82 83 1.966451 CCCAACCGGAGAGCAACAC 60.966 63.158 9.46 0.00 0.00 3.32
83 84 1.966451 CCAACCGGAGAGCAACACC 60.966 63.158 9.46 0.00 0.00 4.16
90 91 2.674796 GGAGAGCAACACCGACTTAT 57.325 50.000 0.00 0.00 0.00 1.73
91 92 2.271800 GGAGAGCAACACCGACTTATG 58.728 52.381 0.00 0.00 0.00 1.90
92 93 2.094182 GGAGAGCAACACCGACTTATGA 60.094 50.000 0.00 0.00 0.00 2.15
93 94 2.924290 GAGAGCAACACCGACTTATGAC 59.076 50.000 0.00 0.00 0.00 3.06
94 95 2.299013 AGAGCAACACCGACTTATGACA 59.701 45.455 0.00 0.00 0.00 3.58
95 96 2.668457 GAGCAACACCGACTTATGACAG 59.332 50.000 0.00 0.00 0.00 3.51
96 97 1.732259 GCAACACCGACTTATGACAGG 59.268 52.381 0.00 0.00 0.00 4.00
97 98 2.611971 GCAACACCGACTTATGACAGGA 60.612 50.000 0.00 0.00 0.00 3.86
98 99 2.993899 CAACACCGACTTATGACAGGAC 59.006 50.000 0.00 0.00 0.00 3.85
99 100 2.526432 ACACCGACTTATGACAGGACT 58.474 47.619 0.00 0.00 0.00 3.85
100 101 2.897969 ACACCGACTTATGACAGGACTT 59.102 45.455 0.00 0.00 0.00 3.01
101 102 3.254060 CACCGACTTATGACAGGACTTG 58.746 50.000 0.00 0.00 0.00 3.16
102 103 2.233922 ACCGACTTATGACAGGACTTGG 59.766 50.000 0.00 0.00 0.00 3.61
103 104 2.418746 CCGACTTATGACAGGACTTGGG 60.419 54.545 0.00 0.00 0.00 4.12
104 105 2.633488 GACTTATGACAGGACTTGGGC 58.367 52.381 0.00 0.00 0.00 5.36
105 106 1.282157 ACTTATGACAGGACTTGGGCC 59.718 52.381 0.00 0.00 0.00 5.80
106 107 0.623723 TTATGACAGGACTTGGGCCC 59.376 55.000 17.59 17.59 0.00 5.80
107 108 0.253160 TATGACAGGACTTGGGCCCT 60.253 55.000 25.70 1.15 0.00 5.19
108 109 1.566298 ATGACAGGACTTGGGCCCTC 61.566 60.000 25.70 12.68 0.00 4.30
109 110 1.920835 GACAGGACTTGGGCCCTCT 60.921 63.158 25.70 9.73 0.00 3.69
110 111 1.904990 GACAGGACTTGGGCCCTCTC 61.905 65.000 25.70 14.11 0.00 3.20
111 112 2.285743 AGGACTTGGGCCCTCTCC 60.286 66.667 25.70 22.28 0.00 3.71
112 113 3.412408 GGACTTGGGCCCTCTCCC 61.412 72.222 25.70 15.37 46.73 4.30
113 114 3.412408 GACTTGGGCCCTCTCCCC 61.412 72.222 25.70 3.40 45.97 4.81
129 130 3.577389 CCCCCAAAAGACTAGCCTG 57.423 57.895 0.00 0.00 0.00 4.85
130 131 0.698818 CCCCCAAAAGACTAGCCTGT 59.301 55.000 0.00 0.00 0.00 4.00
131 132 1.075536 CCCCCAAAAGACTAGCCTGTT 59.924 52.381 0.00 0.00 0.00 3.16
132 133 2.307686 CCCCCAAAAGACTAGCCTGTTA 59.692 50.000 0.00 0.00 0.00 2.41
133 134 3.610911 CCCCAAAAGACTAGCCTGTTAG 58.389 50.000 0.00 0.00 0.00 2.34
134 135 3.610911 CCCAAAAGACTAGCCTGTTAGG 58.389 50.000 0.00 0.00 38.80 2.69
135 136 3.263425 CCCAAAAGACTAGCCTGTTAGGA 59.737 47.826 0.00 0.00 37.67 2.94
136 137 4.508662 CCAAAAGACTAGCCTGTTAGGAG 58.491 47.826 0.00 0.00 37.67 3.69
137 138 4.508662 CAAAAGACTAGCCTGTTAGGAGG 58.491 47.826 0.00 0.00 37.67 4.30
138 139 2.463047 AGACTAGCCTGTTAGGAGGG 57.537 55.000 0.00 0.00 37.67 4.30
139 140 1.062810 AGACTAGCCTGTTAGGAGGGG 60.063 57.143 0.00 0.00 37.67 4.79
140 141 1.016415 ACTAGCCTGTTAGGAGGGGA 58.984 55.000 0.00 0.00 37.67 4.81
141 142 1.343176 ACTAGCCTGTTAGGAGGGGAC 60.343 57.143 0.00 0.00 37.67 4.46
142 143 0.714180 TAGCCTGTTAGGAGGGGACA 59.286 55.000 0.00 0.00 37.67 4.02
143 144 0.910088 AGCCTGTTAGGAGGGGACAC 60.910 60.000 0.00 0.00 37.67 3.67
144 145 1.911702 GCCTGTTAGGAGGGGACACC 61.912 65.000 0.00 0.00 37.67 4.16
162 163 1.370064 CCCCCGCCCTTATAAGTCG 59.630 63.158 11.50 12.97 0.00 4.18
163 164 1.405272 CCCCCGCCCTTATAAGTCGT 61.405 60.000 11.50 0.00 0.00 4.34
164 165 0.249741 CCCCGCCCTTATAAGTCGTG 60.250 60.000 11.50 7.40 0.00 4.35
165 166 0.462789 CCCGCCCTTATAAGTCGTGT 59.537 55.000 11.50 0.00 0.00 4.49
166 167 1.134610 CCCGCCCTTATAAGTCGTGTT 60.135 52.381 11.50 0.00 0.00 3.32
167 168 2.101249 CCCGCCCTTATAAGTCGTGTTA 59.899 50.000 11.50 0.00 0.00 2.41
168 169 3.243975 CCCGCCCTTATAAGTCGTGTTAT 60.244 47.826 11.50 0.00 0.00 1.89
169 170 3.739300 CCGCCCTTATAAGTCGTGTTATG 59.261 47.826 11.50 0.00 0.00 1.90
170 171 4.365723 CGCCCTTATAAGTCGTGTTATGT 58.634 43.478 11.50 0.00 0.00 2.29
171 172 4.443394 CGCCCTTATAAGTCGTGTTATGTC 59.557 45.833 11.50 0.00 0.00 3.06
172 173 5.598769 GCCCTTATAAGTCGTGTTATGTCT 58.401 41.667 11.50 0.00 0.00 3.41
173 174 5.690857 GCCCTTATAAGTCGTGTTATGTCTC 59.309 44.000 11.50 0.00 0.00 3.36
174 175 6.214399 CCCTTATAAGTCGTGTTATGTCTCC 58.786 44.000 11.50 0.00 0.00 3.71
175 176 6.214399 CCTTATAAGTCGTGTTATGTCTCCC 58.786 44.000 11.50 0.00 0.00 4.30
176 177 4.667519 ATAAGTCGTGTTATGTCTCCCC 57.332 45.455 0.00 0.00 0.00 4.81
177 178 1.192428 AGTCGTGTTATGTCTCCCCC 58.808 55.000 0.00 0.00 0.00 5.40
199 200 2.774687 ACAACCGATGTGGGACTAAAC 58.225 47.619 0.00 0.00 41.93 2.01
200 201 2.081462 CAACCGATGTGGGACTAAACC 58.919 52.381 0.00 0.00 44.64 3.27
212 213 4.353383 GGACTAAACCCAACAGACTTCT 57.647 45.455 0.00 0.00 0.00 2.85
226 227 5.968387 CAGACTTCTGTAAAGAACAACGT 57.032 39.130 0.00 0.00 37.74 3.99
227 228 5.728255 CAGACTTCTGTAAAGAACAACGTG 58.272 41.667 0.00 0.00 37.74 4.49
228 229 5.518847 CAGACTTCTGTAAAGAACAACGTGA 59.481 40.000 0.00 0.00 37.74 4.35
229 230 6.201044 CAGACTTCTGTAAAGAACAACGTGAT 59.799 38.462 0.00 0.00 37.74 3.06
230 231 6.761714 AGACTTCTGTAAAGAACAACGTGATT 59.238 34.615 0.00 0.00 37.74 2.57
231 232 6.945072 ACTTCTGTAAAGAACAACGTGATTC 58.055 36.000 4.29 4.29 37.74 2.52
232 233 6.761714 ACTTCTGTAAAGAACAACGTGATTCT 59.238 34.615 8.41 8.41 37.74 2.40
233 234 7.924412 ACTTCTGTAAAGAACAACGTGATTCTA 59.076 33.333 13.36 0.00 37.74 2.10
234 235 8.651391 TTCTGTAAAGAACAACGTGATTCTAA 57.349 30.769 13.36 4.60 37.74 2.10
235 236 8.294341 TCTGTAAAGAACAACGTGATTCTAAG 57.706 34.615 13.36 9.74 37.74 2.18
236 237 8.139350 TCTGTAAAGAACAACGTGATTCTAAGA 58.861 33.333 13.36 11.32 37.74 2.10
237 238 8.294341 TGTAAAGAACAACGTGATTCTAAGAG 57.706 34.615 13.36 0.00 34.01 2.85
238 239 8.139350 TGTAAAGAACAACGTGATTCTAAGAGA 58.861 33.333 13.36 1.17 34.01 3.10
239 240 7.644986 AAAGAACAACGTGATTCTAAGAGAG 57.355 36.000 13.36 0.00 34.01 3.20
240 241 6.576662 AGAACAACGTGATTCTAAGAGAGA 57.423 37.500 11.77 0.00 33.35 3.10
241 242 7.164230 AGAACAACGTGATTCTAAGAGAGAT 57.836 36.000 11.77 0.00 33.35 2.75
242 243 7.254852 AGAACAACGTGATTCTAAGAGAGATC 58.745 38.462 11.77 0.00 33.35 2.75
243 244 6.516739 ACAACGTGATTCTAAGAGAGATCA 57.483 37.500 0.00 0.00 32.88 2.92
244 245 6.559810 ACAACGTGATTCTAAGAGAGATCAG 58.440 40.000 0.00 0.00 32.88 2.90
245 246 6.375736 ACAACGTGATTCTAAGAGAGATCAGA 59.624 38.462 0.00 0.00 32.88 3.27
246 247 7.094162 ACAACGTGATTCTAAGAGAGATCAGAA 60.094 37.037 0.00 0.00 32.88 3.02
247 248 7.026631 ACGTGATTCTAAGAGAGATCAGAAG 57.973 40.000 0.00 0.00 32.88 2.85
248 249 5.914635 CGTGATTCTAAGAGAGATCAGAAGC 59.085 44.000 0.00 0.00 34.76 3.86
249 250 6.459435 CGTGATTCTAAGAGAGATCAGAAGCA 60.459 42.308 5.38 5.38 40.12 3.91
250 251 6.804677 TGATTCTAAGAGAGATCAGAAGCAC 58.195 40.000 5.38 0.00 38.20 4.40
251 252 6.379417 TGATTCTAAGAGAGATCAGAAGCACA 59.621 38.462 5.38 0.69 38.20 4.57
252 253 6.596309 TTCTAAGAGAGATCAGAAGCACAA 57.404 37.500 0.00 0.00 32.88 3.33
253 254 6.596309 TCTAAGAGAGATCAGAAGCACAAA 57.404 37.500 0.00 0.00 0.00 2.83
254 255 6.997655 TCTAAGAGAGATCAGAAGCACAAAA 58.002 36.000 0.00 0.00 0.00 2.44
255 256 7.619050 TCTAAGAGAGATCAGAAGCACAAAAT 58.381 34.615 0.00 0.00 0.00 1.82
256 257 6.497785 AAGAGAGATCAGAAGCACAAAATG 57.502 37.500 0.00 0.00 0.00 2.32
257 258 4.942483 AGAGAGATCAGAAGCACAAAATGG 59.058 41.667 0.00 0.00 0.00 3.16
258 259 4.660168 AGAGATCAGAAGCACAAAATGGT 58.340 39.130 0.00 0.00 42.22 3.55
266 267 1.857837 AGCACAAAATGGTTTTTCGCG 59.142 42.857 0.00 0.00 34.57 5.87
274 275 5.574815 AAATGGTTTTTCGCGATTCAAAG 57.425 34.783 10.88 0.00 0.00 2.77
276 277 3.884169 TGGTTTTTCGCGATTCAAAGAG 58.116 40.909 10.88 0.00 0.00 2.85
277 278 3.234386 GGTTTTTCGCGATTCAAAGAGG 58.766 45.455 10.88 0.00 0.00 3.69
287 289 4.063689 CGATTCAAAGAGGCAGCTATCAT 58.936 43.478 0.00 0.00 0.00 2.45
291 293 5.357742 TCAAAGAGGCAGCTATCATGTTA 57.642 39.130 0.00 0.00 0.00 2.41
317 319 1.509162 GGCGCGTGCTTTCTTTACG 60.509 57.895 21.89 0.00 42.25 3.18
320 322 1.572447 GCGTGCTTTCTTTACGGCA 59.428 52.632 0.00 0.00 38.20 5.69
322 324 1.790481 GCGTGCTTTCTTTACGGCATC 60.790 52.381 0.00 0.00 38.20 3.91
338 340 0.515564 CATCGTGGAAACGTGGAACC 59.484 55.000 0.00 0.00 0.00 3.62
339 341 0.947180 ATCGTGGAAACGTGGAACCG 60.947 55.000 0.00 0.00 0.00 4.44
348 350 2.865343 ACGTGGAACCGTCATCTATC 57.135 50.000 0.00 0.00 35.95 2.08
351 353 1.067212 GTGGAACCGTCATCTATCGCT 59.933 52.381 0.00 0.00 0.00 4.93
353 355 1.337071 GGAACCGTCATCTATCGCTCA 59.663 52.381 0.00 0.00 0.00 4.26
354 356 2.386249 GAACCGTCATCTATCGCTCAC 58.614 52.381 0.00 0.00 0.00 3.51
355 357 1.389555 ACCGTCATCTATCGCTCACA 58.610 50.000 0.00 0.00 0.00 3.58
356 358 1.065701 ACCGTCATCTATCGCTCACAC 59.934 52.381 0.00 0.00 0.00 3.82
357 359 1.389853 CGTCATCTATCGCTCACACG 58.610 55.000 0.00 0.00 0.00 4.49
472 561 0.784778 CGACAGCTCGTTCCTTTCAC 59.215 55.000 0.00 0.00 35.00 3.18
482 571 3.057019 CGTTCCTTTCACATCGAGACAA 58.943 45.455 0.00 0.00 0.00 3.18
485 574 5.444122 GTTCCTTTCACATCGAGACAAAAG 58.556 41.667 0.00 0.00 0.00 2.27
487 576 3.189287 CCTTTCACATCGAGACAAAAGGG 59.811 47.826 17.82 4.85 39.24 3.95
489 578 0.804989 CACATCGAGACAAAAGGGCC 59.195 55.000 0.00 0.00 0.00 5.80
490 579 0.400213 ACATCGAGACAAAAGGGCCA 59.600 50.000 6.18 0.00 0.00 5.36
491 580 1.004745 ACATCGAGACAAAAGGGCCAT 59.995 47.619 6.18 0.00 0.00 4.40
492 581 1.402968 CATCGAGACAAAAGGGCCATG 59.597 52.381 6.18 4.16 0.00 3.66
493 582 0.400213 TCGAGACAAAAGGGCCATGT 59.600 50.000 6.18 7.94 0.00 3.21
500 589 1.545582 CAAAAGGGCCATGTGAACGAT 59.454 47.619 6.18 0.00 0.00 3.73
539 628 9.985730 AAAATCAATAAAGCTCTTTGAATCACA 57.014 25.926 9.23 0.00 33.45 3.58
540 629 8.976986 AATCAATAAAGCTCTTTGAATCACAC 57.023 30.769 9.23 0.00 33.45 3.82
541 630 7.509141 TCAATAAAGCTCTTTGAATCACACA 57.491 32.000 5.21 0.00 34.23 3.72
602 691 5.473066 TTAACTTAGGTTAGTCTTGGCGT 57.527 39.130 0.00 0.00 38.86 5.68
625 714 5.461737 GTCGTGATGGCTTTTCAAAAATCAA 59.538 36.000 0.00 0.00 0.00 2.57
626 715 6.146021 GTCGTGATGGCTTTTCAAAAATCAAT 59.854 34.615 0.00 0.00 0.00 2.57
627 716 6.705381 TCGTGATGGCTTTTCAAAAATCAATT 59.295 30.769 0.00 0.00 0.00 2.32
628 717 7.226325 TCGTGATGGCTTTTCAAAAATCAATTT 59.774 29.630 0.00 0.00 0.00 1.82
671 764 4.402155 AGCTGACCAGTTGAAACAAAATCA 59.598 37.500 0.00 0.00 0.00 2.57
689 782 0.659427 CATCAACGATGCGCCATCTT 59.341 50.000 4.18 0.00 38.59 2.40
700 793 0.879400 CGCCATCTTAGCTGCCTCTG 60.879 60.000 0.00 0.00 0.00 3.35
725 818 1.880027 GTCTTCGTGCCCAGACAAATT 59.120 47.619 0.00 0.00 39.49 1.82
737 830 1.371337 GACAAATTACCCGGCCGGTC 61.371 60.000 40.52 25.51 43.58 4.79
738 831 2.116533 CAAATTACCCGGCCGGTCC 61.117 63.158 40.52 2.02 43.58 4.46
789 883 4.803426 CTCCGACTGCGACCCTGC 62.803 72.222 0.00 0.00 40.82 4.85
801 895 4.020617 CCCTGCAGGCGGTTCAGA 62.021 66.667 28.39 0.00 0.00 3.27
804 898 4.329545 TGCAGGCGGTTCAGACCC 62.330 66.667 0.00 0.00 43.42 4.46
850 944 2.166584 GAACCCGCACCGAAAACGAG 62.167 60.000 0.00 0.00 0.00 4.18
854 948 1.487231 CGCACCGAAAACGAGTCAG 59.513 57.895 0.00 0.00 0.00 3.51
909 1003 3.640407 TGGAGCCAGCCAGTCACC 61.640 66.667 0.00 0.00 33.10 4.02
914 1008 3.579302 CCAGCCAGTCACCCCCAA 61.579 66.667 0.00 0.00 0.00 4.12
915 1009 2.282462 CAGCCAGTCACCCCCAAC 60.282 66.667 0.00 0.00 0.00 3.77
916 1010 2.450502 AGCCAGTCACCCCCAACT 60.451 61.111 0.00 0.00 0.00 3.16
917 1011 2.282462 GCCAGTCACCCCCAACTG 60.282 66.667 0.00 0.00 42.04 3.16
918 1012 2.282462 CCAGTCACCCCCAACTGC 60.282 66.667 0.00 0.00 41.24 4.40
919 1013 2.515398 CAGTCACCCCCAACTGCA 59.485 61.111 0.00 0.00 36.76 4.41
920 1014 1.152777 CAGTCACCCCCAACTGCAA 60.153 57.895 0.00 0.00 36.76 4.08
921 1015 0.540365 CAGTCACCCCCAACTGCAAT 60.540 55.000 0.00 0.00 36.76 3.56
922 1016 0.540365 AGTCACCCCCAACTGCAATG 60.540 55.000 0.00 0.00 0.00 2.82
923 1017 1.907807 TCACCCCCAACTGCAATGC 60.908 57.895 0.00 0.00 0.00 3.56
924 1018 2.200930 ACCCCCAACTGCAATGCA 59.799 55.556 7.99 7.99 36.92 3.96
1014 1129 0.101759 GCTCCATCGCATTTGCACAT 59.898 50.000 3.13 0.00 42.21 3.21
1052 1167 0.463833 AGATCGCCCATTTCGTTCCC 60.464 55.000 0.00 0.00 0.00 3.97
1089 1205 1.756408 TTCGTCCGGCCCACAAGTTA 61.756 55.000 0.00 0.00 0.00 2.24
1124 1241 1.522355 CGCCATCGCCATGTCTTCT 60.522 57.895 0.00 0.00 0.00 2.85
1134 1251 1.395954 CCATGTCTTCTACGACGACGA 59.604 52.381 15.32 0.00 42.66 4.20
1137 1254 0.710567 GTCTTCTACGACGACGACGA 59.289 55.000 25.15 6.73 42.66 4.20
1139 1256 0.247067 CTTCTACGACGACGACGACC 60.247 60.000 25.15 4.43 42.66 4.79
1140 1257 1.944699 TTCTACGACGACGACGACCG 61.945 60.000 25.15 17.71 42.66 4.79
1141 1258 4.134187 TACGACGACGACGACCGC 62.134 66.667 25.15 0.00 43.32 5.68
1203 1320 1.602237 GCCATCCGTGGGAAGAAGA 59.398 57.895 0.00 0.00 46.14 2.87
1410 1527 3.391382 CTCGTCTCACCCACCCCC 61.391 72.222 0.00 0.00 0.00 5.40
1466 1584 9.106070 ACTACGTTTCTTAGTTCAATTCTTGTT 57.894 29.630 0.00 0.00 0.00 2.83
1468 1586 7.415229 ACGTTTCTTAGTTCAATTCTTGTTCC 58.585 34.615 0.00 0.00 0.00 3.62
1473 1591 7.386851 TCTTAGTTCAATTCTTGTTCCGAGAT 58.613 34.615 0.00 0.00 0.00 2.75
1475 1593 9.319143 CTTAGTTCAATTCTTGTTCCGAGATAT 57.681 33.333 0.00 0.00 0.00 1.63
1483 1601 6.844696 TCTTGTTCCGAGATATTTATGCAC 57.155 37.500 0.00 0.00 0.00 4.57
1515 1633 7.060421 TGGTTGAACTTTTCTTCATTAGTCCT 58.940 34.615 0.00 0.00 30.19 3.85
1664 1784 6.460781 ACCGAGAATTCAAGTACACACATTA 58.539 36.000 8.44 0.00 0.00 1.90
1797 1950 8.954950 AGAATCAAGTGATATGAAGTAACCAG 57.045 34.615 0.00 0.00 33.73 4.00
1862 2016 1.519455 CTCGATCCTTCGGTGTGCC 60.519 63.158 0.00 0.00 45.53 5.01
1932 2098 0.937699 GAACCGCAAGTTTTTCGGGC 60.938 55.000 11.29 1.90 46.78 6.13
1967 2133 4.082625 TCCTTGATGATCATGTTGTGCAAC 60.083 41.667 14.30 8.01 41.50 4.17
2091 2258 0.381089 GTGTACTCCTCATCCGTCCG 59.619 60.000 0.00 0.00 0.00 4.79
2093 2260 1.102222 GTACTCCTCATCCGTCCGCT 61.102 60.000 0.00 0.00 0.00 5.52
2136 2303 2.484264 GCTGTTGTTGCTCCTTATCGTT 59.516 45.455 0.00 0.00 0.00 3.85
2138 2305 3.734463 TGTTGTTGCTCCTTATCGTTCA 58.266 40.909 0.00 0.00 0.00 3.18
2154 2321 2.671351 CGTTCAAGTAGAGCATCACCGT 60.671 50.000 0.00 0.00 37.82 4.83
2179 2346 1.372623 GAACGACGGAGGTGTGGAC 60.373 63.158 0.00 0.00 0.00 4.02
2233 2400 3.367992 CATGATCTGGAACTCTCCTCG 57.632 52.381 0.00 0.00 42.94 4.63
2263 2430 3.614399 CGAAGGAGAGCCACTTGTT 57.386 52.632 0.00 0.00 36.29 2.83
2264 2431 2.743636 CGAAGGAGAGCCACTTGTTA 57.256 50.000 0.00 0.00 36.29 2.41
2265 2432 2.611518 CGAAGGAGAGCCACTTGTTAG 58.388 52.381 0.00 0.00 36.29 2.34
2266 2433 2.028930 CGAAGGAGAGCCACTTGTTAGT 60.029 50.000 0.00 0.00 36.29 2.24
2275 2442 3.132925 GCCACTTGTTAGTTGTTACGGA 58.867 45.455 0.00 0.00 30.26 4.69
2278 2445 4.753107 CCACTTGTTAGTTGTTACGGATGT 59.247 41.667 0.00 0.00 30.26 3.06
2288 2455 2.288579 TGTTACGGATGTCGAACTTGCT 60.289 45.455 0.00 0.00 42.43 3.91
2295 2462 3.002042 GGATGTCGAACTTGCTCATCATG 59.998 47.826 10.83 0.00 37.29 3.07
2319 2486 2.612285 TGAGCAGAGGAAAGGAGAGA 57.388 50.000 0.00 0.00 0.00 3.10
2322 2489 2.166254 GAGCAGAGGAAAGGAGAGACAG 59.834 54.545 0.00 0.00 0.00 3.51
2326 2493 0.178891 AGGAAAGGAGAGACAGGGCA 60.179 55.000 0.00 0.00 0.00 5.36
2388 2555 4.496840 GCGCGGCCAAACTACTTAAATAAT 60.497 41.667 8.83 0.00 0.00 1.28
2392 2559 5.295045 CGGCCAAACTACTTAAATAATCGGT 59.705 40.000 2.24 0.00 0.00 4.69
2394 2561 5.969435 GCCAAACTACTTAAATAATCGGTGC 59.031 40.000 0.00 0.00 0.00 5.01
2445 2612 0.810016 ACGGTCGAAGTAGGCTTCTC 59.190 55.000 0.00 0.00 46.65 2.87
2473 2670 2.981977 TTTGGTCACGTCGGCCTGAC 62.982 60.000 13.18 13.18 44.53 3.51
2475 2672 3.986006 GTCACGTCGGCCTGACCA 61.986 66.667 18.07 4.17 45.23 4.02
2504 2701 4.367023 GTAGGTGACCGCCACGCA 62.367 66.667 0.00 0.00 46.62 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.674269 GACCCGGGATTGCGTAACAA 60.674 55.000 32.02 0.00 44.01 2.83
5 6 1.078988 GACCCGGGATTGCGTAACA 60.079 57.895 32.02 0.00 0.00 2.41
6 7 1.816679 GGACCCGGGATTGCGTAAC 60.817 63.158 32.02 6.20 0.00 2.50
7 8 2.585698 GGACCCGGGATTGCGTAA 59.414 61.111 32.02 0.00 0.00 3.18
8 9 3.840594 CGGACCCGGGATTGCGTA 61.841 66.667 32.02 0.00 35.56 4.42
11 12 3.178540 ATAGCGGACCCGGGATTGC 62.179 63.158 32.02 25.98 40.19 3.56
12 13 1.004918 GATAGCGGACCCGGGATTG 60.005 63.158 32.02 16.99 40.19 2.67
13 14 1.458777 TGATAGCGGACCCGGGATT 60.459 57.895 32.02 4.94 40.19 3.01
14 15 2.200370 TGATAGCGGACCCGGGAT 59.800 61.111 32.02 12.15 40.19 3.85
15 16 2.836360 GTGATAGCGGACCCGGGA 60.836 66.667 32.02 2.68 40.19 5.14
16 17 3.925090 GGTGATAGCGGACCCGGG 61.925 72.222 22.25 22.25 40.19 5.73
17 18 3.151710 TGGTGATAGCGGACCCGG 61.152 66.667 10.70 0.00 40.19 5.73
18 19 2.417516 CTGGTGATAGCGGACCCG 59.582 66.667 3.73 3.73 43.09 5.28
19 20 2.109181 GCTGGTGATAGCGGACCC 59.891 66.667 0.00 0.00 33.46 4.46
37 38 1.908066 GACGCATGTGGGTCGGAAAC 61.908 60.000 11.65 0.00 45.66 2.78
38 39 1.669760 GACGCATGTGGGTCGGAAA 60.670 57.895 11.65 0.00 45.66 3.13
39 40 2.047655 GACGCATGTGGGTCGGAA 60.048 61.111 11.65 0.00 45.66 4.30
44 45 1.600636 CTGGTTGACGCATGTGGGT 60.601 57.895 11.65 2.09 44.25 4.51
45 46 2.334946 CCTGGTTGACGCATGTGGG 61.335 63.158 11.65 0.00 0.00 4.61
46 47 2.981560 GCCTGGTTGACGCATGTGG 61.982 63.158 11.65 0.00 0.00 4.17
47 48 2.562912 GCCTGGTTGACGCATGTG 59.437 61.111 4.30 4.30 0.00 3.21
48 49 2.672996 GGCCTGGTTGACGCATGT 60.673 61.111 0.00 0.00 0.00 3.21
49 50 3.443045 GGGCCTGGTTGACGCATG 61.443 66.667 0.84 0.00 0.00 4.06
50 51 3.505790 TTGGGCCTGGTTGACGCAT 62.506 57.895 4.53 0.00 0.00 4.73
51 52 4.196778 TTGGGCCTGGTTGACGCA 62.197 61.111 4.53 0.00 0.00 5.24
52 53 3.670377 GTTGGGCCTGGTTGACGC 61.670 66.667 4.53 0.00 0.00 5.19
53 54 2.983592 GGTTGGGCCTGGTTGACG 60.984 66.667 4.53 0.00 0.00 4.35
54 55 2.983592 CGGTTGGGCCTGGTTGAC 60.984 66.667 4.53 0.00 34.25 3.18
55 56 4.278513 CCGGTTGGGCCTGGTTGA 62.279 66.667 4.53 0.00 34.25 3.18
56 57 4.278513 TCCGGTTGGGCCTGGTTG 62.279 66.667 4.53 0.00 34.18 3.77
57 58 3.966543 CTCCGGTTGGGCCTGGTT 61.967 66.667 4.53 0.00 34.18 3.67
58 59 4.974438 TCTCCGGTTGGGCCTGGT 62.974 66.667 4.53 0.00 34.18 4.00
59 60 4.101448 CTCTCCGGTTGGGCCTGG 62.101 72.222 4.53 1.31 35.24 4.45
60 61 4.785453 GCTCTCCGGTTGGGCCTG 62.785 72.222 4.53 0.00 35.24 4.85
62 63 4.344865 TTGCTCTCCGGTTGGGCC 62.345 66.667 16.84 0.00 35.24 5.80
63 64 3.056328 GTTGCTCTCCGGTTGGGC 61.056 66.667 13.66 13.66 35.24 5.36
64 65 1.966451 GTGTTGCTCTCCGGTTGGG 60.966 63.158 0.00 0.00 35.24 4.12
65 66 1.966451 GGTGTTGCTCTCCGGTTGG 60.966 63.158 0.00 0.00 0.00 3.77
66 67 2.317609 CGGTGTTGCTCTCCGGTTG 61.318 63.158 0.00 0.00 45.75 3.77
67 68 2.030562 CGGTGTTGCTCTCCGGTT 59.969 61.111 0.00 0.00 45.75 4.44
71 72 2.094182 TCATAAGTCGGTGTTGCTCTCC 60.094 50.000 0.00 0.00 0.00 3.71
72 73 2.924290 GTCATAAGTCGGTGTTGCTCTC 59.076 50.000 0.00 0.00 0.00 3.20
73 74 2.299013 TGTCATAAGTCGGTGTTGCTCT 59.701 45.455 0.00 0.00 0.00 4.09
74 75 2.668457 CTGTCATAAGTCGGTGTTGCTC 59.332 50.000 0.00 0.00 0.00 4.26
75 76 2.612972 CCTGTCATAAGTCGGTGTTGCT 60.613 50.000 0.00 0.00 0.00 3.91
76 77 1.732259 CCTGTCATAAGTCGGTGTTGC 59.268 52.381 0.00 0.00 0.00 4.17
77 78 2.993899 GTCCTGTCATAAGTCGGTGTTG 59.006 50.000 0.00 0.00 0.00 3.33
78 79 2.897969 AGTCCTGTCATAAGTCGGTGTT 59.102 45.455 0.00 0.00 0.00 3.32
79 80 2.526432 AGTCCTGTCATAAGTCGGTGT 58.474 47.619 0.00 0.00 0.00 4.16
80 81 3.254060 CAAGTCCTGTCATAAGTCGGTG 58.746 50.000 0.00 0.00 0.00 4.94
81 82 2.233922 CCAAGTCCTGTCATAAGTCGGT 59.766 50.000 0.00 0.00 0.00 4.69
82 83 2.418746 CCCAAGTCCTGTCATAAGTCGG 60.419 54.545 0.00 0.00 0.00 4.79
83 84 2.893637 CCCAAGTCCTGTCATAAGTCG 58.106 52.381 0.00 0.00 0.00 4.18
84 85 2.633488 GCCCAAGTCCTGTCATAAGTC 58.367 52.381 0.00 0.00 0.00 3.01
85 86 1.282157 GGCCCAAGTCCTGTCATAAGT 59.718 52.381 0.00 0.00 0.00 2.24
86 87 1.408822 GGGCCCAAGTCCTGTCATAAG 60.409 57.143 19.95 0.00 33.65 1.73
87 88 0.623723 GGGCCCAAGTCCTGTCATAA 59.376 55.000 19.95 0.00 33.65 1.90
88 89 2.307153 GGGCCCAAGTCCTGTCATA 58.693 57.895 19.95 0.00 33.65 2.15
89 90 3.090765 GGGCCCAAGTCCTGTCAT 58.909 61.111 19.95 0.00 33.65 3.06
111 112 0.698818 ACAGGCTAGTCTTTTGGGGG 59.301 55.000 0.00 0.00 0.00 5.40
112 113 2.586648 AACAGGCTAGTCTTTTGGGG 57.413 50.000 0.00 0.00 0.00 4.96
113 114 3.263425 TCCTAACAGGCTAGTCTTTTGGG 59.737 47.826 17.14 17.14 34.61 4.12
114 115 4.508662 CTCCTAACAGGCTAGTCTTTTGG 58.491 47.826 6.00 2.88 34.61 3.28
115 116 4.508662 CCTCCTAACAGGCTAGTCTTTTG 58.491 47.826 6.00 0.00 34.61 2.44
116 117 3.519913 CCCTCCTAACAGGCTAGTCTTTT 59.480 47.826 0.00 0.00 34.61 2.27
117 118 3.108376 CCCTCCTAACAGGCTAGTCTTT 58.892 50.000 0.00 0.00 34.61 2.52
118 119 2.627217 CCCCTCCTAACAGGCTAGTCTT 60.627 54.545 0.00 0.00 34.61 3.01
119 120 1.062810 CCCCTCCTAACAGGCTAGTCT 60.063 57.143 0.00 0.00 34.61 3.24
120 121 1.063114 TCCCCTCCTAACAGGCTAGTC 60.063 57.143 0.00 0.00 34.61 2.59
121 122 1.016415 TCCCCTCCTAACAGGCTAGT 58.984 55.000 0.00 0.00 34.61 2.57
122 123 1.343075 TGTCCCCTCCTAACAGGCTAG 60.343 57.143 0.00 0.00 34.61 3.42
123 124 0.714180 TGTCCCCTCCTAACAGGCTA 59.286 55.000 0.00 0.00 34.61 3.93
124 125 0.910088 GTGTCCCCTCCTAACAGGCT 60.910 60.000 0.00 0.00 34.61 4.58
125 126 1.602771 GTGTCCCCTCCTAACAGGC 59.397 63.158 0.00 0.00 34.61 4.85
126 127 2.297937 GGTGTCCCCTCCTAACAGG 58.702 63.158 0.00 0.00 36.46 4.00
144 145 1.370064 CGACTTATAAGGGCGGGGG 59.630 63.158 16.73 0.00 0.00 5.40
145 146 0.249741 CACGACTTATAAGGGCGGGG 60.250 60.000 24.35 16.28 33.96 5.73
146 147 0.462789 ACACGACTTATAAGGGCGGG 59.537 55.000 22.67 22.67 37.36 6.13
147 148 2.304751 AACACGACTTATAAGGGCGG 57.695 50.000 24.35 18.04 33.96 6.13
148 149 4.365723 ACATAACACGACTTATAAGGGCG 58.634 43.478 21.15 21.15 35.18 6.13
149 150 5.598769 AGACATAACACGACTTATAAGGGC 58.401 41.667 16.73 7.37 0.00 5.19
150 151 6.214399 GGAGACATAACACGACTTATAAGGG 58.786 44.000 16.73 10.26 0.00 3.95
151 152 6.214399 GGGAGACATAACACGACTTATAAGG 58.786 44.000 16.73 2.57 0.00 2.69
152 153 6.214399 GGGGAGACATAACACGACTTATAAG 58.786 44.000 11.05 11.05 0.00 1.73
153 154 5.069516 GGGGGAGACATAACACGACTTATAA 59.930 44.000 0.00 0.00 0.00 0.98
154 155 4.586001 GGGGGAGACATAACACGACTTATA 59.414 45.833 0.00 0.00 0.00 0.98
155 156 3.387050 GGGGGAGACATAACACGACTTAT 59.613 47.826 0.00 0.00 0.00 1.73
156 157 2.762327 GGGGGAGACATAACACGACTTA 59.238 50.000 0.00 0.00 0.00 2.24
157 158 1.553704 GGGGGAGACATAACACGACTT 59.446 52.381 0.00 0.00 0.00 3.01
158 159 1.192428 GGGGGAGACATAACACGACT 58.808 55.000 0.00 0.00 0.00 4.18
159 160 3.754766 GGGGGAGACATAACACGAC 57.245 57.895 0.00 0.00 0.00 4.34
179 180 2.551504 GGTTTAGTCCCACATCGGTTGT 60.552 50.000 0.00 0.00 39.91 3.32
180 181 2.081462 GGTTTAGTCCCACATCGGTTG 58.919 52.381 0.00 0.00 0.00 3.77
181 182 1.003928 GGGTTTAGTCCCACATCGGTT 59.996 52.381 0.00 0.00 46.30 4.44
182 183 0.616891 GGGTTTAGTCCCACATCGGT 59.383 55.000 0.00 0.00 46.30 4.69
183 184 3.471354 GGGTTTAGTCCCACATCGG 57.529 57.895 0.00 0.00 46.30 4.18
189 190 7.437911 CAGAAGTCTGTTGGGTTTAGTCCCA 62.438 48.000 0.00 0.00 45.14 4.37
190 191 5.042905 CAGAAGTCTGTTGGGTTTAGTCCC 61.043 50.000 0.00 0.00 41.98 4.46
191 192 4.065789 CAGAAGTCTGTTGGGTTTAGTCC 58.934 47.826 0.00 0.00 39.09 3.85
205 206 5.657474 TCACGTTGTTCTTTACAGAAGTCT 58.343 37.500 0.00 0.00 39.86 3.24
206 207 5.961395 TCACGTTGTTCTTTACAGAAGTC 57.039 39.130 0.00 0.00 39.86 3.01
207 208 6.761714 AGAATCACGTTGTTCTTTACAGAAGT 59.238 34.615 6.41 0.00 39.86 3.01
208 209 7.178712 AGAATCACGTTGTTCTTTACAGAAG 57.821 36.000 6.41 0.00 39.86 2.85
209 210 8.651391 TTAGAATCACGTTGTTCTTTACAGAA 57.349 30.769 15.14 3.04 38.19 3.02
210 211 8.139350 TCTTAGAATCACGTTGTTCTTTACAGA 58.861 33.333 15.14 10.11 38.19 3.41
211 212 8.294341 TCTTAGAATCACGTTGTTCTTTACAG 57.706 34.615 15.14 8.53 38.19 2.74
212 213 8.139350 TCTCTTAGAATCACGTTGTTCTTTACA 58.861 33.333 15.14 0.00 36.23 2.41
213 214 8.516811 TCTCTTAGAATCACGTTGTTCTTTAC 57.483 34.615 15.14 0.00 36.23 2.01
214 215 8.573885 TCTCTCTTAGAATCACGTTGTTCTTTA 58.426 33.333 15.14 6.02 36.23 1.85
215 216 7.434492 TCTCTCTTAGAATCACGTTGTTCTTT 58.566 34.615 15.14 0.00 36.23 2.52
216 217 6.982852 TCTCTCTTAGAATCACGTTGTTCTT 58.017 36.000 15.14 3.40 36.23 2.52
217 218 6.576662 TCTCTCTTAGAATCACGTTGTTCT 57.423 37.500 14.53 14.53 38.22 3.01
218 219 7.030165 TGATCTCTCTTAGAATCACGTTGTTC 58.970 38.462 0.00 0.00 37.89 3.18
219 220 6.925211 TGATCTCTCTTAGAATCACGTTGTT 58.075 36.000 0.00 0.00 37.89 2.83
220 221 6.375736 TCTGATCTCTCTTAGAATCACGTTGT 59.624 38.462 0.00 0.00 37.89 3.32
221 222 6.790282 TCTGATCTCTCTTAGAATCACGTTG 58.210 40.000 0.00 0.00 37.89 4.10
222 223 7.397892 TTCTGATCTCTCTTAGAATCACGTT 57.602 36.000 0.00 0.00 37.89 3.99
223 224 6.459573 GCTTCTGATCTCTCTTAGAATCACGT 60.460 42.308 0.00 0.00 37.89 4.49
224 225 5.914635 GCTTCTGATCTCTCTTAGAATCACG 59.085 44.000 0.00 0.00 37.89 4.35
225 226 6.697019 GTGCTTCTGATCTCTCTTAGAATCAC 59.303 42.308 8.53 8.53 38.37 3.06
226 227 6.379417 TGTGCTTCTGATCTCTCTTAGAATCA 59.621 38.462 0.00 0.00 37.89 2.57
227 228 6.804677 TGTGCTTCTGATCTCTCTTAGAATC 58.195 40.000 0.00 0.00 37.89 2.52
228 229 6.788598 TGTGCTTCTGATCTCTCTTAGAAT 57.211 37.500 0.00 0.00 37.89 2.40
229 230 6.596309 TTGTGCTTCTGATCTCTCTTAGAA 57.404 37.500 0.00 0.00 37.89 2.10
230 231 6.596309 TTTGTGCTTCTGATCTCTCTTAGA 57.404 37.500 0.00 0.00 39.02 2.10
231 232 7.201626 CCATTTTGTGCTTCTGATCTCTCTTAG 60.202 40.741 0.00 0.00 0.00 2.18
232 233 6.596888 CCATTTTGTGCTTCTGATCTCTCTTA 59.403 38.462 0.00 0.00 0.00 2.10
233 234 5.415077 CCATTTTGTGCTTCTGATCTCTCTT 59.585 40.000 0.00 0.00 0.00 2.85
234 235 4.942483 CCATTTTGTGCTTCTGATCTCTCT 59.058 41.667 0.00 0.00 0.00 3.10
235 236 4.699257 ACCATTTTGTGCTTCTGATCTCTC 59.301 41.667 0.00 0.00 0.00 3.20
236 237 4.660168 ACCATTTTGTGCTTCTGATCTCT 58.340 39.130 0.00 0.00 0.00 3.10
237 238 5.382618 AACCATTTTGTGCTTCTGATCTC 57.617 39.130 0.00 0.00 0.00 2.75
238 239 5.796424 AAACCATTTTGTGCTTCTGATCT 57.204 34.783 0.00 0.00 0.00 2.75
239 240 6.346040 CGAAAAACCATTTTGTGCTTCTGATC 60.346 38.462 0.00 0.00 38.83 2.92
240 241 5.463061 CGAAAAACCATTTTGTGCTTCTGAT 59.537 36.000 0.00 0.00 38.83 2.90
241 242 4.803088 CGAAAAACCATTTTGTGCTTCTGA 59.197 37.500 0.00 0.00 38.83 3.27
242 243 4.550639 GCGAAAAACCATTTTGTGCTTCTG 60.551 41.667 0.00 0.00 38.83 3.02
243 244 3.555547 GCGAAAAACCATTTTGTGCTTCT 59.444 39.130 0.00 0.00 38.83 2.85
244 245 3.601360 CGCGAAAAACCATTTTGTGCTTC 60.601 43.478 0.00 0.00 38.83 3.86
245 246 2.283884 CGCGAAAAACCATTTTGTGCTT 59.716 40.909 0.00 0.00 38.83 3.91
246 247 1.857837 CGCGAAAAACCATTTTGTGCT 59.142 42.857 0.00 0.00 38.83 4.40
247 248 1.855360 TCGCGAAAAACCATTTTGTGC 59.145 42.857 6.20 0.00 38.83 4.57
248 249 4.208047 TGAATCGCGAAAAACCATTTTGTG 59.792 37.500 15.24 0.00 38.83 3.33
249 250 4.363999 TGAATCGCGAAAAACCATTTTGT 58.636 34.783 15.24 0.00 38.83 2.83
250 251 4.963237 TGAATCGCGAAAAACCATTTTG 57.037 36.364 15.24 0.00 38.83 2.44
251 252 5.751028 TCTTTGAATCGCGAAAAACCATTTT 59.249 32.000 15.24 0.00 41.37 1.82
252 253 5.285651 TCTTTGAATCGCGAAAAACCATTT 58.714 33.333 15.24 0.00 0.00 2.32
253 254 4.865776 TCTTTGAATCGCGAAAAACCATT 58.134 34.783 15.24 0.00 0.00 3.16
254 255 4.475944 CTCTTTGAATCGCGAAAAACCAT 58.524 39.130 15.24 0.00 0.00 3.55
255 256 3.304391 CCTCTTTGAATCGCGAAAAACCA 60.304 43.478 15.24 3.92 0.00 3.67
256 257 3.234386 CCTCTTTGAATCGCGAAAAACC 58.766 45.455 15.24 0.97 0.00 3.27
257 258 2.656897 GCCTCTTTGAATCGCGAAAAAC 59.343 45.455 15.24 5.55 0.00 2.43
258 259 2.292016 TGCCTCTTTGAATCGCGAAAAA 59.708 40.909 15.24 13.45 0.00 1.94
259 260 1.876799 TGCCTCTTTGAATCGCGAAAA 59.123 42.857 15.24 8.74 0.00 2.29
260 261 1.464608 CTGCCTCTTTGAATCGCGAAA 59.535 47.619 15.24 0.00 0.00 3.46
261 262 1.078709 CTGCCTCTTTGAATCGCGAA 58.921 50.000 15.24 0.00 0.00 4.70
262 263 1.361668 GCTGCCTCTTTGAATCGCGA 61.362 55.000 13.09 13.09 0.00 5.87
266 267 4.820716 ACATGATAGCTGCCTCTTTGAATC 59.179 41.667 0.00 0.00 0.00 2.52
274 275 2.408050 CGGTAACATGATAGCTGCCTC 58.592 52.381 10.03 0.00 0.00 4.70
276 277 1.512926 CCGGTAACATGATAGCTGCC 58.487 55.000 10.03 0.00 0.00 4.85
277 278 0.868406 GCCGGTAACATGATAGCTGC 59.132 55.000 11.58 11.58 0.00 5.25
327 329 3.977489 CGATAGATGACGGTTCCACGTTT 60.977 47.826 0.00 0.00 43.83 3.60
328 330 2.479049 CGATAGATGACGGTTCCACGTT 60.479 50.000 0.00 0.00 43.83 3.99
338 340 1.389853 CGTGTGAGCGATAGATGACG 58.610 55.000 0.00 0.00 43.14 4.35
339 341 1.333931 TCCGTGTGAGCGATAGATGAC 59.666 52.381 0.00 0.00 39.71 3.06
355 357 0.098905 CACGAGTGATCACGATCCGT 59.901 55.000 19.85 21.67 42.36 4.69
356 358 0.592500 CCACGAGTGATCACGATCCG 60.593 60.000 19.85 21.11 37.02 4.18
357 359 0.738975 TCCACGAGTGATCACGATCC 59.261 55.000 19.85 9.78 37.02 3.36
392 394 4.961511 GTGGCAGTGACGCGGACA 62.962 66.667 12.47 7.72 0.00 4.02
419 422 2.290916 GCTATGTCGTCTCTTCCGATCA 59.709 50.000 0.00 0.00 36.62 2.92
423 426 2.783828 ATGCTATGTCGTCTCTTCCG 57.216 50.000 0.00 0.00 0.00 4.30
472 561 1.402968 CATGGCCCTTTTGTCTCGATG 59.597 52.381 0.00 0.00 0.00 3.84
482 571 1.176527 CATCGTTCACATGGCCCTTT 58.823 50.000 0.00 0.00 0.00 3.11
485 574 0.965363 AACCATCGTTCACATGGCCC 60.965 55.000 0.00 0.00 44.32 5.80
487 576 3.206150 AGATAACCATCGTTCACATGGC 58.794 45.455 0.00 0.00 44.32 4.40
489 578 7.713764 TTGATAGATAACCATCGTTCACATG 57.286 36.000 0.00 0.00 36.20 3.21
490 579 8.731275 TTTTGATAGATAACCATCGTTCACAT 57.269 30.769 0.00 0.00 36.20 3.21
491 580 8.554835 TTTTTGATAGATAACCATCGTTCACA 57.445 30.769 0.00 0.00 36.20 3.58
492 581 9.651718 GATTTTTGATAGATAACCATCGTTCAC 57.348 33.333 0.00 0.00 36.20 3.18
493 582 9.389755 TGATTTTTGATAGATAACCATCGTTCA 57.610 29.630 0.00 0.00 36.20 3.18
548 637 5.048846 TGGAAGAGTAGTTTTCAGCCTTT 57.951 39.130 3.48 0.00 0.00 3.11
580 669 5.473039 GACGCCAAGACTAACCTAAGTTAA 58.527 41.667 0.00 0.00 37.99 2.01
581 670 4.379813 CGACGCCAAGACTAACCTAAGTTA 60.380 45.833 0.00 0.00 37.42 2.24
582 671 3.613432 CGACGCCAAGACTAACCTAAGTT 60.613 47.826 0.00 0.00 40.15 2.66
595 684 1.577328 AAAGCCATCACGACGCCAAG 61.577 55.000 0.00 0.00 0.00 3.61
602 691 5.193663 TGATTTTTGAAAAGCCATCACGA 57.806 34.783 2.44 0.00 33.60 4.35
648 741 4.402155 TGATTTTGTTTCAACTGGTCAGCT 59.598 37.500 0.00 0.00 0.00 4.24
649 742 4.681744 TGATTTTGTTTCAACTGGTCAGC 58.318 39.130 0.00 0.00 0.00 4.26
650 743 6.506147 TGATGATTTTGTTTCAACTGGTCAG 58.494 36.000 0.00 0.00 0.00 3.51
651 744 6.462552 TGATGATTTTGTTTCAACTGGTCA 57.537 33.333 0.00 0.00 0.00 4.02
652 745 6.074888 CGTTGATGATTTTGTTTCAACTGGTC 60.075 38.462 11.49 0.00 43.55 4.02
671 764 2.138320 CTAAGATGGCGCATCGTTGAT 58.862 47.619 10.83 1.13 44.67 2.57
689 782 1.930251 AGACAAGACAGAGGCAGCTA 58.070 50.000 0.00 0.00 0.00 3.32
700 793 0.033504 TCTGGGCACGAAGACAAGAC 59.966 55.000 0.00 0.00 0.00 3.01
739 832 3.719144 CCAAAACCGACGGGCGAC 61.719 66.667 20.00 0.00 44.57 5.19
740 833 4.238654 ACCAAAACCGACGGGCGA 62.239 61.111 20.00 0.00 44.57 5.54
741 834 3.719144 GACCAAAACCGACGGGCG 61.719 66.667 20.00 0.00 36.48 6.13
742 835 2.592287 TGACCAAAACCGACGGGC 60.592 61.111 20.00 0.00 36.48 6.13
743 836 1.964373 CCTGACCAAAACCGACGGG 60.964 63.158 20.00 1.77 40.11 5.28
801 895 2.285368 TTGGAGCGGATCTGGGGT 60.285 61.111 3.14 0.00 0.00 4.95
804 898 1.361668 CGTTGTTGGAGCGGATCTGG 61.362 60.000 3.14 0.00 0.00 3.86
840 934 1.773496 GCGTCTGACTCGTTTTCGG 59.227 57.895 6.21 0.00 44.25 4.30
909 1003 1.342174 GGATATGCATTGCAGTTGGGG 59.658 52.381 17.52 0.00 43.65 4.96
913 1007 4.139786 CAGGTAGGATATGCATTGCAGTT 58.860 43.478 17.52 6.65 43.65 3.16
914 1008 3.497405 CCAGGTAGGATATGCATTGCAGT 60.497 47.826 17.52 8.20 40.59 4.40
915 1009 3.079578 CCAGGTAGGATATGCATTGCAG 58.920 50.000 17.52 0.00 40.59 4.41
916 1010 2.815215 GCCAGGTAGGATATGCATTGCA 60.815 50.000 14.72 14.72 41.30 4.08
917 1011 1.815003 GCCAGGTAGGATATGCATTGC 59.185 52.381 3.54 0.46 41.22 3.56
918 1012 2.224843 TGGCCAGGTAGGATATGCATTG 60.225 50.000 3.54 0.00 41.22 2.82
919 1013 2.065007 TGGCCAGGTAGGATATGCATT 58.935 47.619 3.54 0.00 41.22 3.56
920 1014 1.352352 GTGGCCAGGTAGGATATGCAT 59.648 52.381 5.11 3.79 41.22 3.96
921 1015 0.764890 GTGGCCAGGTAGGATATGCA 59.235 55.000 5.11 0.00 41.22 3.96
922 1016 0.036875 GGTGGCCAGGTAGGATATGC 59.963 60.000 5.11 0.00 41.22 3.14
923 1017 1.734655 AGGTGGCCAGGTAGGATATG 58.265 55.000 5.11 0.00 41.22 1.78
924 1018 2.339769 GAAGGTGGCCAGGTAGGATAT 58.660 52.381 5.11 0.00 41.22 1.63
1014 1129 4.467084 GATGCCAGCGAACGGGGA 62.467 66.667 0.00 0.00 35.62 4.81
1052 1167 3.181534 ACGAACGAACTTGTATGATTGCG 60.182 43.478 0.14 0.00 0.00 4.85
1089 1205 1.023513 GCGCAGGCTTGATCTCAACT 61.024 55.000 0.30 0.00 35.83 3.16
1124 1241 4.134187 GCGGTCGTCGTCGTCGTA 62.134 66.667 11.41 0.00 41.72 3.43
1235 1352 0.692476 CTCCCATCTGGTGTTGGTGA 59.308 55.000 0.00 0.00 32.53 4.02
1457 1575 8.345565 GTGCATAAATATCTCGGAACAAGAATT 58.654 33.333 0.00 0.00 0.00 2.17
1458 1576 7.498900 TGTGCATAAATATCTCGGAACAAGAAT 59.501 33.333 0.00 0.00 0.00 2.40
1466 1584 6.479990 CAGAGTTTGTGCATAAATATCTCGGA 59.520 38.462 17.82 0.00 0.00 4.55
1468 1586 6.258727 ACCAGAGTTTGTGCATAAATATCTCG 59.741 38.462 17.82 15.35 0.00 4.04
1473 1591 7.230510 AGTTCAACCAGAGTTTGTGCATAAATA 59.769 33.333 12.01 0.00 32.45 1.40
1475 1593 5.359576 AGTTCAACCAGAGTTTGTGCATAAA 59.640 36.000 4.30 4.30 32.45 1.40
1483 1601 6.620678 TGAAGAAAAGTTCAACCAGAGTTTG 58.379 36.000 0.00 0.00 33.41 2.93
1533 1651 8.319146 AGTCCTTTTTATTTCGAGAGTATGGAA 58.681 33.333 0.00 0.00 0.00 3.53
1568 1686 9.218440 GATGAATTGGCAAAATTCTCCTTTTTA 57.782 29.630 19.15 3.59 37.50 1.52
1636 1756 6.134061 GTGTGTACTTGAATTCTCGGTTTTC 58.866 40.000 7.05 0.00 0.00 2.29
1642 1762 8.495949 ACTTTAATGTGTGTACTTGAATTCTCG 58.504 33.333 7.05 0.12 0.00 4.04
1695 1819 8.674263 TTGTGTTTGAAATTTGAATGGCTAAT 57.326 26.923 0.00 0.00 0.00 1.73
1797 1950 5.392380 CCAAGAAGATATTGTTGAGCACCAC 60.392 44.000 11.22 0.00 0.00 4.16
1862 2016 5.352569 GGAACATCACTCCAACAGAATACAG 59.647 44.000 0.00 0.00 32.77 2.74
1975 2141 3.997021 CCTGTAGAAGGTCATGACAACAC 59.003 47.826 26.47 15.80 41.74 3.32
2073 2240 1.381928 GCGGACGGATGAGGAGTACA 61.382 60.000 0.00 0.00 0.00 2.90
2077 2244 2.725008 GAGCGGACGGATGAGGAG 59.275 66.667 0.00 0.00 0.00 3.69
2091 2258 3.655810 CTCCACACAGAGGCCGAGC 62.656 68.421 0.00 0.00 0.00 5.03
2093 2260 2.997315 CCTCCACACAGAGGCCGA 60.997 66.667 0.00 0.00 46.76 5.54
2119 2286 4.385825 ACTTGAACGATAAGGAGCAACAA 58.614 39.130 0.00 0.00 0.00 2.83
2122 2289 5.651530 CTCTACTTGAACGATAAGGAGCAA 58.348 41.667 0.00 0.00 36.29 3.91
2136 2303 1.132453 CGACGGTGATGCTCTACTTGA 59.868 52.381 0.00 0.00 0.00 3.02
2138 2305 1.132643 GACGACGGTGATGCTCTACTT 59.867 52.381 0.00 0.00 0.00 2.24
2172 2339 4.065281 CTCGTCGGGGGTCCACAC 62.065 72.222 0.00 0.00 0.00 3.82
2204 2371 3.646976 CAGATCATGGCGCCGCTG 61.647 66.667 23.90 21.54 0.00 5.18
2205 2372 4.923942 CCAGATCATGGCGCCGCT 62.924 66.667 23.90 9.04 43.83 5.52
2248 2415 2.706190 ACAACTAACAAGTGGCTCTCCT 59.294 45.455 0.00 0.00 0.00 3.69
2254 2421 3.132925 TCCGTAACAACTAACAAGTGGC 58.867 45.455 0.00 0.00 0.00 5.01
2260 2427 4.502171 TCGACATCCGTAACAACTAACA 57.498 40.909 0.00 0.00 39.75 2.41
2261 2428 4.919754 AGTTCGACATCCGTAACAACTAAC 59.080 41.667 0.00 0.00 39.75 2.34
2262 2429 5.125100 AGTTCGACATCCGTAACAACTAA 57.875 39.130 0.00 0.00 39.75 2.24
2263 2430 4.771590 AGTTCGACATCCGTAACAACTA 57.228 40.909 0.00 0.00 39.75 2.24
2264 2431 3.655276 AGTTCGACATCCGTAACAACT 57.345 42.857 0.00 0.00 39.75 3.16
2265 2432 3.663493 GCAAGTTCGACATCCGTAACAAC 60.663 47.826 0.00 0.00 39.75 3.32
2266 2433 2.477375 GCAAGTTCGACATCCGTAACAA 59.523 45.455 0.00 0.00 39.75 2.83
2275 2442 2.941064 CCATGATGAGCAAGTTCGACAT 59.059 45.455 0.00 0.00 0.00 3.06
2278 2445 1.372582 GCCATGATGAGCAAGTTCGA 58.627 50.000 0.00 0.00 0.00 3.71
2295 2462 0.813210 CCTTTCCTCTGCTCATCGCC 60.813 60.000 0.00 0.00 38.05 5.54
2308 2475 0.693049 TTGCCCTGTCTCTCCTTTCC 59.307 55.000 0.00 0.00 0.00 3.13
2314 2481 2.125350 CGCCTTGCCCTGTCTCTC 60.125 66.667 0.00 0.00 0.00 3.20
2319 2486 4.684134 AATGCCGCCTTGCCCTGT 62.684 61.111 0.00 0.00 0.00 4.00
2322 2489 4.440127 CACAATGCCGCCTTGCCC 62.440 66.667 8.16 0.00 0.00 5.36
2326 2493 2.652530 CTTGCACAATGCCGCCTT 59.347 55.556 0.00 0.00 44.23 4.35
2334 2501 1.366319 ACCTCCTCTCCTTGCACAAT 58.634 50.000 0.00 0.00 0.00 2.71
2374 2541 5.296035 GCCTGCACCGATTATTTAAGTAGTT 59.704 40.000 0.00 0.00 0.00 2.24
2378 2545 2.612212 CGCCTGCACCGATTATTTAAGT 59.388 45.455 0.00 0.00 0.00 2.24
2473 2670 2.019249 CACCTACCACATTCATGCTGG 58.981 52.381 0.00 6.79 36.05 4.85
2475 2672 2.991250 GTCACCTACCACATTCATGCT 58.009 47.619 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.