Multiple sequence alignment - TraesCS7B01G225000

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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 TraesCS7B01G225000 chr7B 100.000 2684 0 0 1 2684 425409090 425411773 0.000000e+00 4957
1 TraesCS7B01G225000 chr7B 91.772 158 6 7 1 155 451687444 451687597 2.090000e-51 213
2 TraesCS7B01G225000 chr7D 93.171 2387 105 15 324 2684 410115346 410112992 0.000000e+00 3452
3 TraesCS7B01G225000 chr7A 96.034 1311 47 4 540 1846 471817010 471818319 0.000000e+00 2128
4 TraesCS7B01G225000 chr7A 87.046 826 85 11 1871 2682 471818400 471819217 0.000000e+00 913
5 TraesCS7B01G225000 chr7A 78.261 391 78 6 1871 2254 493916775 493917165 7.420000e-61 244
6 TraesCS7B01G225000 chr5A 78.718 827 137 30 1882 2684 639085601 639086412 1.420000e-142 516
7 TraesCS7B01G225000 chr3B 79.973 739 109 21 1966 2680 275917035 275917758 2.380000e-140 508
8 TraesCS7B01G225000 chr3B 88.995 209 23 0 120 328 383484768 383484560 2.650000e-65 259
9 TraesCS7B01G225000 chr3B 100.000 127 0 0 1 127 101891769 101891643 4.470000e-58 235
10 TraesCS7B01G225000 chr3A 78.726 832 120 33 1880 2679 262526573 262527379 1.110000e-138 503
11 TraesCS7B01G225000 chr3D 78.151 833 133 27 1882 2683 192055180 192054366 4.020000e-133 484
12 TraesCS7B01G225000 chr2B 77.041 845 151 27 1871 2684 727592651 727591819 1.900000e-121 446
13 TraesCS7B01G225000 chr2B 98.462 130 2 0 1 130 363282273 363282402 2.080000e-56 230
14 TraesCS7B01G225000 chr6B 91.388 209 18 0 120 328 545250559 545250351 1.220000e-73 287
15 TraesCS7B01G225000 chr6B 98.473 131 2 0 1 131 348647755 348647885 5.780000e-57 231
16 TraesCS7B01G225000 chr6B 84.076 157 22 3 1871 2025 145011777 145011932 5.990000e-32 148
17 TraesCS7B01G225000 chr4B 99.219 128 1 0 1 128 124072139 124072266 5.780000e-57 231
18 TraesCS7B01G225000 chr4B 99.213 127 1 0 1 127 268725615 268725741 2.080000e-56 230
19 TraesCS7B01G225000 chr4B 99.213 127 1 0 1 127 481508719 481508593 2.080000e-56 230
20 TraesCS7B01G225000 chr1B 99.213 127 1 0 1 127 310074241 310074367 2.080000e-56 230
21 TraesCS7B01G225000 chr1B 99.213 127 1 0 1 127 330257062 330257188 2.080000e-56 230


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 TraesCS7B01G225000 chr7B 425409090 425411773 2683 False 4957.0 4957 100.000 1 2684 1 chr7B.!!$F1 2683
1 TraesCS7B01G225000 chr7D 410112992 410115346 2354 True 3452.0 3452 93.171 324 2684 1 chr7D.!!$R1 2360
2 TraesCS7B01G225000 chr7A 471817010 471819217 2207 False 1520.5 2128 91.540 540 2682 2 chr7A.!!$F2 2142
3 TraesCS7B01G225000 chr5A 639085601 639086412 811 False 516.0 516 78.718 1882 2684 1 chr5A.!!$F1 802
4 TraesCS7B01G225000 chr3B 275917035 275917758 723 False 508.0 508 79.973 1966 2680 1 chr3B.!!$F1 714
5 TraesCS7B01G225000 chr3A 262526573 262527379 806 False 503.0 503 78.726 1880 2679 1 chr3A.!!$F1 799
6 TraesCS7B01G225000 chr3D 192054366 192055180 814 True 484.0 484 78.151 1882 2683 1 chr3D.!!$R1 801
7 TraesCS7B01G225000 chr2B 727591819 727592651 832 True 446.0 446 77.041 1871 2684 1 chr2B.!!$R1 813

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
179 180 0.034756 GCACCATTTGGGGTTGAACC 59.965 55.0 5.62 5.62 41.84 3.62 F
429 430 0.161024 GAAACCTCGTGCTTTCGACG 59.839 55.0 0.00 0.00 38.20 5.12 F
636 652 0.179234 TTCAGGCAGTTCCGTGTCAA 59.821 50.0 0.00 0.00 40.77 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1188 1213 1.003718 GAAAGCCAGCACCGTACCT 60.004 57.895 0.0 0.0 0.0 3.08 R
1494 1519 1.004440 GTTCTTGTCTCTGGCCGCT 60.004 57.895 0.0 0.0 0.0 5.52 R
2391 2522 1.156736 CTTCGACTTGCCAAATCCGT 58.843 50.000 0.0 0.0 0.0 4.69 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
20 21 3.674906 CTCTATCGAGAGGGCCCG 58.325 66.667 18.44 4.06 44.92 6.13
21 22 1.073373 CTCTATCGAGAGGGCCCGA 59.927 63.158 18.44 10.63 44.92 5.14
22 23 0.537600 CTCTATCGAGAGGGCCCGAA 60.538 60.000 18.44 1.01 44.92 4.30
23 24 0.822532 TCTATCGAGAGGGCCCGAAC 60.823 60.000 18.44 12.45 38.36 3.95
24 25 1.807495 CTATCGAGAGGGCCCGAACC 61.807 65.000 18.44 7.31 38.36 3.62
25 26 2.294170 TATCGAGAGGGCCCGAACCT 62.294 60.000 18.44 12.55 42.18 3.50
26 27 4.148825 CGAGAGGGCCCGAACCTG 62.149 72.222 18.44 1.23 38.79 4.00
27 28 3.787001 GAGAGGGCCCGAACCTGG 61.787 72.222 18.44 0.00 38.79 4.45
36 37 1.984066 CCCGAACCTGGGTAAAAACA 58.016 50.000 0.00 0.00 44.76 2.83
37 38 2.521126 CCCGAACCTGGGTAAAAACAT 58.479 47.619 0.00 0.00 44.76 2.71
38 39 2.490509 CCCGAACCTGGGTAAAAACATC 59.509 50.000 0.00 0.00 44.76 3.06
39 40 2.160813 CCGAACCTGGGTAAAAACATCG 59.839 50.000 0.00 0.00 0.00 3.84
40 41 2.809696 CGAACCTGGGTAAAAACATCGT 59.190 45.455 0.00 0.00 0.00 3.73
41 42 3.364565 CGAACCTGGGTAAAAACATCGTG 60.365 47.826 0.00 0.00 0.00 4.35
42 43 3.217681 ACCTGGGTAAAAACATCGTGT 57.782 42.857 0.00 0.00 0.00 4.49
43 44 3.143728 ACCTGGGTAAAAACATCGTGTC 58.856 45.455 0.00 0.00 0.00 3.67
44 45 2.486592 CCTGGGTAAAAACATCGTGTCC 59.513 50.000 0.00 0.00 0.00 4.02
45 46 2.486592 CTGGGTAAAAACATCGTGTCCC 59.513 50.000 0.00 0.00 31.92 4.46
46 47 2.106857 TGGGTAAAAACATCGTGTCCCT 59.893 45.455 10.79 0.00 32.37 4.20
47 48 3.151554 GGGTAAAAACATCGTGTCCCTT 58.848 45.455 0.00 0.00 29.50 3.95
48 49 3.057806 GGGTAAAAACATCGTGTCCCTTG 60.058 47.826 0.00 0.00 29.50 3.61
49 50 3.566742 GGTAAAAACATCGTGTCCCTTGT 59.433 43.478 0.00 0.00 0.00 3.16
50 51 3.982576 AAAAACATCGTGTCCCTTGTC 57.017 42.857 0.00 0.00 0.00 3.18
51 52 2.930826 AAACATCGTGTCCCTTGTCT 57.069 45.000 0.00 0.00 0.00 3.41
52 53 2.457366 AACATCGTGTCCCTTGTCTC 57.543 50.000 0.00 0.00 0.00 3.36
53 54 0.608640 ACATCGTGTCCCTTGTCTCC 59.391 55.000 0.00 0.00 0.00 3.71
54 55 0.898320 CATCGTGTCCCTTGTCTCCT 59.102 55.000 0.00 0.00 0.00 3.69
55 56 0.898320 ATCGTGTCCCTTGTCTCCTG 59.102 55.000 0.00 0.00 0.00 3.86
56 57 0.469331 TCGTGTCCCTTGTCTCCTGT 60.469 55.000 0.00 0.00 0.00 4.00
57 58 0.393077 CGTGTCCCTTGTCTCCTGTT 59.607 55.000 0.00 0.00 0.00 3.16
58 59 1.616865 CGTGTCCCTTGTCTCCTGTTA 59.383 52.381 0.00 0.00 0.00 2.41
59 60 2.609737 CGTGTCCCTTGTCTCCTGTTAC 60.610 54.545 0.00 0.00 0.00 2.50
60 61 1.975680 TGTCCCTTGTCTCCTGTTACC 59.024 52.381 0.00 0.00 0.00 2.85
61 62 1.975680 GTCCCTTGTCTCCTGTTACCA 59.024 52.381 0.00 0.00 0.00 3.25
62 63 2.572104 GTCCCTTGTCTCCTGTTACCAT 59.428 50.000 0.00 0.00 0.00 3.55
63 64 2.838202 TCCCTTGTCTCCTGTTACCATC 59.162 50.000 0.00 0.00 0.00 3.51
64 65 2.092914 CCCTTGTCTCCTGTTACCATCC 60.093 54.545 0.00 0.00 0.00 3.51
65 66 2.418746 CCTTGTCTCCTGTTACCATCCG 60.419 54.545 0.00 0.00 0.00 4.18
66 67 0.535335 TGTCTCCTGTTACCATCCGC 59.465 55.000 0.00 0.00 0.00 5.54
67 68 0.179081 GTCTCCTGTTACCATCCGCC 60.179 60.000 0.00 0.00 0.00 6.13
68 69 0.325296 TCTCCTGTTACCATCCGCCT 60.325 55.000 0.00 0.00 0.00 5.52
69 70 1.063492 TCTCCTGTTACCATCCGCCTA 60.063 52.381 0.00 0.00 0.00 3.93
70 71 1.341531 CTCCTGTTACCATCCGCCTAG 59.658 57.143 0.00 0.00 0.00 3.02
71 72 1.063492 TCCTGTTACCATCCGCCTAGA 60.063 52.381 0.00 0.00 0.00 2.43
72 73 1.068741 CCTGTTACCATCCGCCTAGAC 59.931 57.143 0.00 0.00 0.00 2.59
73 74 0.742505 TGTTACCATCCGCCTAGACG 59.257 55.000 0.00 0.00 0.00 4.18
74 75 0.596859 GTTACCATCCGCCTAGACGC 60.597 60.000 0.00 0.00 0.00 5.19
75 76 1.038681 TTACCATCCGCCTAGACGCA 61.039 55.000 0.00 0.00 0.00 5.24
76 77 1.731433 TACCATCCGCCTAGACGCAC 61.731 60.000 0.00 0.00 0.00 5.34
77 78 2.494445 CATCCGCCTAGACGCACA 59.506 61.111 0.00 0.00 0.00 4.57
78 79 1.589993 CATCCGCCTAGACGCACAG 60.590 63.158 0.00 0.00 0.00 3.66
79 80 2.052690 ATCCGCCTAGACGCACAGT 61.053 57.895 0.00 0.00 0.00 3.55
80 81 1.605058 ATCCGCCTAGACGCACAGTT 61.605 55.000 0.00 0.00 0.00 3.16
81 82 1.805945 CCGCCTAGACGCACAGTTC 60.806 63.158 0.00 0.00 0.00 3.01
82 83 2.152699 CGCCTAGACGCACAGTTCG 61.153 63.158 0.00 0.00 0.00 3.95
83 84 1.805945 GCCTAGACGCACAGTTCGG 60.806 63.158 0.00 0.00 0.00 4.30
84 85 1.153823 CCTAGACGCACAGTTCGGG 60.154 63.158 0.00 0.00 0.00 5.14
85 86 1.592400 CCTAGACGCACAGTTCGGGA 61.592 60.000 0.00 0.00 0.00 5.14
86 87 0.456312 CTAGACGCACAGTTCGGGAC 60.456 60.000 0.00 0.00 0.00 4.46
87 88 1.870055 TAGACGCACAGTTCGGGACC 61.870 60.000 0.00 0.00 0.00 4.46
88 89 4.309950 ACGCACAGTTCGGGACCC 62.310 66.667 0.00 0.00 0.00 4.46
90 91 4.717313 GCACAGTTCGGGACCCCC 62.717 72.222 4.46 0.00 41.09 5.40
91 92 2.928396 CACAGTTCGGGACCCCCT 60.928 66.667 4.46 0.00 42.67 4.79
92 93 1.611261 CACAGTTCGGGACCCCCTA 60.611 63.158 4.46 0.00 42.67 3.53
93 94 1.611556 ACAGTTCGGGACCCCCTAC 60.612 63.158 4.46 0.29 42.67 3.18
94 95 2.040114 AGTTCGGGACCCCCTACC 59.960 66.667 4.46 0.00 42.67 3.18
95 96 3.085947 GTTCGGGACCCCCTACCC 61.086 72.222 4.46 0.00 42.67 3.69
99 100 3.759101 GGGACCCCCTACCCGAGA 61.759 72.222 0.00 0.00 41.34 4.04
100 101 2.613421 GGACCCCCTACCCGAGAT 59.387 66.667 0.00 0.00 0.00 2.75
101 102 1.533513 GGACCCCCTACCCGAGATC 60.534 68.421 0.00 0.00 0.00 2.75
102 103 1.533513 GACCCCCTACCCGAGATCC 60.534 68.421 0.00 0.00 0.00 3.36
103 104 2.600769 CCCCCTACCCGAGATCCG 60.601 72.222 0.00 0.00 38.18 4.18
104 105 3.303928 CCCCTACCCGAGATCCGC 61.304 72.222 0.00 0.00 36.84 5.54
105 106 3.303928 CCCTACCCGAGATCCGCC 61.304 72.222 0.00 0.00 36.84 6.13
106 107 3.671411 CCTACCCGAGATCCGCCG 61.671 72.222 0.00 0.00 36.84 6.46
107 108 3.671411 CTACCCGAGATCCGCCGG 61.671 72.222 0.00 0.00 44.94 6.13
108 109 4.511246 TACCCGAGATCCGCCGGT 62.511 66.667 1.63 11.60 43.93 5.28
110 111 4.157120 CCCGAGATCCGCCGGTTT 62.157 66.667 1.63 0.00 43.93 3.27
111 112 2.125269 CCGAGATCCGCCGGTTTT 60.125 61.111 1.63 0.00 40.78 2.43
112 113 2.461110 CCGAGATCCGCCGGTTTTG 61.461 63.158 1.63 0.00 40.78 2.44
113 114 1.447140 CGAGATCCGCCGGTTTTGA 60.447 57.895 1.63 0.00 0.00 2.69
114 115 1.693083 CGAGATCCGCCGGTTTTGAC 61.693 60.000 1.63 0.00 0.00 3.18
115 116 0.672401 GAGATCCGCCGGTTTTGACA 60.672 55.000 1.63 0.00 0.00 3.58
116 117 0.953960 AGATCCGCCGGTTTTGACAC 60.954 55.000 1.63 0.00 0.00 3.67
117 118 1.918868 GATCCGCCGGTTTTGACACC 61.919 60.000 1.63 0.00 0.00 4.16
126 127 3.597377 GGTTTTGACACCGACACTAAC 57.403 47.619 0.00 0.00 0.00 2.34
127 128 3.200483 GGTTTTGACACCGACACTAACT 58.800 45.455 0.00 0.00 0.00 2.24
128 129 3.001939 GGTTTTGACACCGACACTAACTG 59.998 47.826 0.00 0.00 0.00 3.16
129 130 3.530265 TTTGACACCGACACTAACTGT 57.470 42.857 0.00 0.00 34.96 3.55
139 140 0.586319 CACTAACTGTGCCGTTGTGG 59.414 55.000 0.00 0.00 40.06 4.17
140 141 0.466543 ACTAACTGTGCCGTTGTGGA 59.533 50.000 0.00 0.00 42.00 4.02
141 142 1.148310 CTAACTGTGCCGTTGTGGAG 58.852 55.000 0.00 0.00 42.00 3.86
142 143 0.250124 TAACTGTGCCGTTGTGGAGG 60.250 55.000 0.00 0.00 42.00 4.30
143 144 1.978455 AACTGTGCCGTTGTGGAGGA 61.978 55.000 0.00 0.00 42.00 3.71
144 145 1.003355 CTGTGCCGTTGTGGAGGAT 60.003 57.895 0.00 0.00 42.00 3.24
145 146 0.606401 CTGTGCCGTTGTGGAGGATT 60.606 55.000 0.00 0.00 42.00 3.01
146 147 0.605319 TGTGCCGTTGTGGAGGATTC 60.605 55.000 0.00 0.00 42.00 2.52
147 148 0.321653 GTGCCGTTGTGGAGGATTCT 60.322 55.000 0.00 0.00 42.00 2.40
148 149 0.036388 TGCCGTTGTGGAGGATTCTC 60.036 55.000 0.00 0.00 42.00 2.87
149 150 0.250513 GCCGTTGTGGAGGATTCTCT 59.749 55.000 0.00 0.00 42.00 3.10
150 151 1.740718 GCCGTTGTGGAGGATTCTCTC 60.741 57.143 0.00 0.00 42.00 3.20
160 161 0.461961 GGATTCTCTCCACCCACTCG 59.538 60.000 0.00 0.00 44.26 4.18
161 162 0.179097 GATTCTCTCCACCCACTCGC 60.179 60.000 0.00 0.00 0.00 5.03
162 163 0.904865 ATTCTCTCCACCCACTCGCA 60.905 55.000 0.00 0.00 0.00 5.10
163 164 1.816863 TTCTCTCCACCCACTCGCAC 61.817 60.000 0.00 0.00 0.00 5.34
164 165 3.302347 CTCTCCACCCACTCGCACC 62.302 68.421 0.00 0.00 0.00 5.01
165 166 3.625897 CTCCACCCACTCGCACCA 61.626 66.667 0.00 0.00 0.00 4.17
166 167 2.927856 TCCACCCACTCGCACCAT 60.928 61.111 0.00 0.00 0.00 3.55
167 168 2.034066 CCACCCACTCGCACCATT 59.966 61.111 0.00 0.00 0.00 3.16
168 169 1.603455 CCACCCACTCGCACCATTT 60.603 57.895 0.00 0.00 0.00 2.32
169 170 1.580942 CACCCACTCGCACCATTTG 59.419 57.895 0.00 0.00 0.00 2.32
170 171 1.603455 ACCCACTCGCACCATTTGG 60.603 57.895 0.00 0.00 42.17 3.28
171 172 2.342650 CCCACTCGCACCATTTGGG 61.343 63.158 0.96 0.00 41.12 4.12
172 173 2.342650 CCACTCGCACCATTTGGGG 61.343 63.158 0.96 0.00 42.91 4.96
173 174 1.603455 CACTCGCACCATTTGGGGT 60.603 57.895 0.00 0.00 41.84 4.95
174 175 1.152830 ACTCGCACCATTTGGGGTT 59.847 52.632 0.00 0.00 41.84 4.11
175 176 1.178534 ACTCGCACCATTTGGGGTTG 61.179 55.000 0.00 0.00 41.84 3.77
176 177 0.893270 CTCGCACCATTTGGGGTTGA 60.893 55.000 0.00 0.00 41.84 3.18
177 178 0.468214 TCGCACCATTTGGGGTTGAA 60.468 50.000 0.00 0.00 41.84 2.69
178 179 0.319469 CGCACCATTTGGGGTTGAAC 60.319 55.000 0.00 0.00 41.84 3.18
179 180 0.034756 GCACCATTTGGGGTTGAACC 59.965 55.000 5.62 5.62 41.84 3.62
193 194 5.582689 GGTTGAACCCTCTCATTTTATGG 57.417 43.478 2.08 0.00 30.04 2.74
194 195 4.142160 GGTTGAACCCTCTCATTTTATGGC 60.142 45.833 2.08 0.00 30.04 4.40
195 196 4.314522 TGAACCCTCTCATTTTATGGCA 57.685 40.909 0.00 0.00 0.00 4.92
196 197 4.870636 TGAACCCTCTCATTTTATGGCAT 58.129 39.130 4.88 4.88 0.00 4.40
197 198 5.271598 TGAACCCTCTCATTTTATGGCATT 58.728 37.500 4.78 0.00 0.00 3.56
198 199 5.360714 TGAACCCTCTCATTTTATGGCATTC 59.639 40.000 4.78 0.00 0.00 2.67
199 200 4.870636 ACCCTCTCATTTTATGGCATTCA 58.129 39.130 4.78 0.00 0.00 2.57
200 201 5.271598 ACCCTCTCATTTTATGGCATTCAA 58.728 37.500 4.78 0.00 0.00 2.69
201 202 5.361857 ACCCTCTCATTTTATGGCATTCAAG 59.638 40.000 4.78 0.00 0.00 3.02
202 203 5.287226 CCTCTCATTTTATGGCATTCAAGC 58.713 41.667 4.78 0.00 0.00 4.01
203 204 5.163488 CCTCTCATTTTATGGCATTCAAGCA 60.163 40.000 4.78 0.00 35.83 3.91
204 205 6.283544 TCTCATTTTATGGCATTCAAGCAA 57.716 33.333 4.78 0.00 35.83 3.91
205 206 6.699366 TCTCATTTTATGGCATTCAAGCAAA 58.301 32.000 4.78 0.00 35.83 3.68
206 207 7.160049 TCTCATTTTATGGCATTCAAGCAAAA 58.840 30.769 4.78 5.66 35.83 2.44
207 208 7.660617 TCTCATTTTATGGCATTCAAGCAAAAA 59.339 29.630 4.78 4.90 35.83 1.94
231 232 7.535489 AATCACAGTTAACCTTATCGTAAGC 57.465 36.000 0.88 0.00 37.18 3.09
232 233 5.413499 TCACAGTTAACCTTATCGTAAGCC 58.587 41.667 0.88 0.00 37.18 4.35
233 234 5.186409 TCACAGTTAACCTTATCGTAAGCCT 59.814 40.000 0.88 0.00 37.18 4.58
234 235 5.873164 CACAGTTAACCTTATCGTAAGCCTT 59.127 40.000 0.88 0.00 37.18 4.35
235 236 6.035758 CACAGTTAACCTTATCGTAAGCCTTC 59.964 42.308 0.88 0.00 37.18 3.46
236 237 6.070938 ACAGTTAACCTTATCGTAAGCCTTCT 60.071 38.462 0.88 0.00 37.18 2.85
237 238 6.817140 CAGTTAACCTTATCGTAAGCCTTCTT 59.183 38.462 0.88 0.00 36.35 2.52
238 239 6.817140 AGTTAACCTTATCGTAAGCCTTCTTG 59.183 38.462 0.88 0.00 33.85 3.02
239 240 5.416271 AACCTTATCGTAAGCCTTCTTGA 57.584 39.130 0.00 0.00 33.85 3.02
240 241 5.416271 ACCTTATCGTAAGCCTTCTTGAA 57.584 39.130 0.00 0.00 33.85 2.69
241 242 5.420409 ACCTTATCGTAAGCCTTCTTGAAG 58.580 41.667 3.55 3.55 33.85 3.02
242 243 5.046520 ACCTTATCGTAAGCCTTCTTGAAGT 60.047 40.000 9.21 0.00 33.85 3.01
243 244 5.520649 CCTTATCGTAAGCCTTCTTGAAGTC 59.479 44.000 9.21 0.00 33.85 3.01
244 245 4.537135 ATCGTAAGCCTTCTTGAAGTCA 57.463 40.909 9.21 0.00 33.85 3.41
245 246 4.330944 TCGTAAGCCTTCTTGAAGTCAA 57.669 40.909 9.21 0.00 33.85 3.18
246 247 4.307432 TCGTAAGCCTTCTTGAAGTCAAG 58.693 43.478 13.80 13.80 45.71 3.02
247 248 4.202223 TCGTAAGCCTTCTTGAAGTCAAGT 60.202 41.667 18.18 3.54 45.10 3.16
248 249 5.684030 TCGTAAGCCTTCTTGAAGTCAAGTT 60.684 40.000 18.18 9.21 45.10 2.66
249 250 7.129066 TCGTAAGCCTTCTTGAAGTCAAGTTT 61.129 38.462 18.18 10.11 45.10 2.66
250 251 8.844468 TCGTAAGCCTTCTTGAAGTCAAGTTTC 61.844 40.741 18.18 8.39 45.10 2.78
259 260 7.441878 CTTGAAGTCAAGTTTCAACACAATC 57.558 36.000 12.09 0.00 46.11 2.67
260 261 5.890334 TGAAGTCAAGTTTCAACACAATCC 58.110 37.500 0.00 0.00 31.98 3.01
261 262 4.918810 AGTCAAGTTTCAACACAATCCC 57.081 40.909 0.00 0.00 0.00 3.85
262 263 3.636764 AGTCAAGTTTCAACACAATCCCC 59.363 43.478 0.00 0.00 0.00 4.81
263 264 2.621055 TCAAGTTTCAACACAATCCCCG 59.379 45.455 0.00 0.00 0.00 5.73
264 265 0.958822 AGTTTCAACACAATCCCCGC 59.041 50.000 0.00 0.00 0.00 6.13
265 266 0.958822 GTTTCAACACAATCCCCGCT 59.041 50.000 0.00 0.00 0.00 5.52
266 267 1.339929 GTTTCAACACAATCCCCGCTT 59.660 47.619 0.00 0.00 0.00 4.68
267 268 1.698506 TTCAACACAATCCCCGCTTT 58.301 45.000 0.00 0.00 0.00 3.51
268 269 1.698506 TCAACACAATCCCCGCTTTT 58.301 45.000 0.00 0.00 0.00 2.27
269 270 2.035632 TCAACACAATCCCCGCTTTTT 58.964 42.857 0.00 0.00 0.00 1.94
289 290 5.756195 TTTTCTTGACTTGAGTGTGATGG 57.244 39.130 0.00 0.00 0.00 3.51
290 291 4.687901 TTCTTGACTTGAGTGTGATGGA 57.312 40.909 0.00 0.00 0.00 3.41
291 292 4.263018 TCTTGACTTGAGTGTGATGGAG 57.737 45.455 0.00 0.00 0.00 3.86
292 293 3.007290 TCTTGACTTGAGTGTGATGGAGG 59.993 47.826 0.00 0.00 0.00 4.30
293 294 2.608623 TGACTTGAGTGTGATGGAGGA 58.391 47.619 0.00 0.00 0.00 3.71
294 295 3.176411 TGACTTGAGTGTGATGGAGGAT 58.824 45.455 0.00 0.00 0.00 3.24
295 296 3.584406 TGACTTGAGTGTGATGGAGGATT 59.416 43.478 0.00 0.00 0.00 3.01
296 297 4.042062 TGACTTGAGTGTGATGGAGGATTT 59.958 41.667 0.00 0.00 0.00 2.17
297 298 4.583871 ACTTGAGTGTGATGGAGGATTTC 58.416 43.478 0.00 0.00 0.00 2.17
298 299 4.042062 ACTTGAGTGTGATGGAGGATTTCA 59.958 41.667 0.00 0.00 0.00 2.69
299 300 4.849813 TGAGTGTGATGGAGGATTTCAT 57.150 40.909 0.00 0.00 0.00 2.57
300 301 4.520179 TGAGTGTGATGGAGGATTTCATG 58.480 43.478 0.00 0.00 0.00 3.07
301 302 3.285484 AGTGTGATGGAGGATTTCATGC 58.715 45.455 0.00 0.00 0.00 4.06
302 303 3.018856 GTGTGATGGAGGATTTCATGCA 58.981 45.455 0.00 0.00 31.59 3.96
303 304 3.444742 GTGTGATGGAGGATTTCATGCAA 59.555 43.478 0.00 0.00 30.68 4.08
304 305 3.697542 TGTGATGGAGGATTTCATGCAAG 59.302 43.478 0.00 0.00 30.68 4.01
305 306 3.067742 GTGATGGAGGATTTCATGCAAGG 59.932 47.826 0.00 0.00 30.68 3.61
306 307 2.905415 TGGAGGATTTCATGCAAGGT 57.095 45.000 0.00 0.00 0.00 3.50
307 308 2.726821 TGGAGGATTTCATGCAAGGTC 58.273 47.619 0.00 0.00 0.00 3.85
308 309 2.041485 TGGAGGATTTCATGCAAGGTCA 59.959 45.455 0.00 0.00 0.00 4.02
309 310 3.091545 GGAGGATTTCATGCAAGGTCAA 58.908 45.455 0.00 0.00 0.00 3.18
310 311 3.129988 GGAGGATTTCATGCAAGGTCAAG 59.870 47.826 0.00 0.00 0.00 3.02
311 312 4.012374 GAGGATTTCATGCAAGGTCAAGA 58.988 43.478 0.00 0.00 0.00 3.02
312 313 4.607239 AGGATTTCATGCAAGGTCAAGAT 58.393 39.130 0.00 0.00 0.00 2.40
313 314 5.021458 AGGATTTCATGCAAGGTCAAGATT 58.979 37.500 0.00 0.00 0.00 2.40
314 315 5.126707 AGGATTTCATGCAAGGTCAAGATTC 59.873 40.000 0.00 0.00 0.00 2.52
315 316 4.789012 TTTCATGCAAGGTCAAGATTCC 57.211 40.909 0.00 0.00 0.00 3.01
316 317 3.438216 TCATGCAAGGTCAAGATTCCA 57.562 42.857 0.00 0.00 0.00 3.53
317 318 3.972133 TCATGCAAGGTCAAGATTCCAT 58.028 40.909 0.00 0.00 0.00 3.41
318 319 3.949754 TCATGCAAGGTCAAGATTCCATC 59.050 43.478 0.00 0.00 0.00 3.51
319 320 2.726821 TGCAAGGTCAAGATTCCATCC 58.273 47.619 0.00 0.00 0.00 3.51
320 321 2.041485 TGCAAGGTCAAGATTCCATCCA 59.959 45.455 0.00 0.00 0.00 3.41
321 322 3.294214 GCAAGGTCAAGATTCCATCCAT 58.706 45.455 0.00 0.00 0.00 3.41
322 323 4.079844 TGCAAGGTCAAGATTCCATCCATA 60.080 41.667 0.00 0.00 0.00 2.74
323 324 4.889409 GCAAGGTCAAGATTCCATCCATAA 59.111 41.667 0.00 0.00 0.00 1.90
324 325 5.537674 GCAAGGTCAAGATTCCATCCATAAT 59.462 40.000 0.00 0.00 0.00 1.28
325 326 6.041296 GCAAGGTCAAGATTCCATCCATAATT 59.959 38.462 0.00 0.00 0.00 1.40
326 327 7.418254 GCAAGGTCAAGATTCCATCCATAATTT 60.418 37.037 0.00 0.00 0.00 1.82
327 328 8.480501 CAAGGTCAAGATTCCATCCATAATTTT 58.519 33.333 0.00 0.00 0.00 1.82
328 329 8.613922 AGGTCAAGATTCCATCCATAATTTTT 57.386 30.769 0.00 0.00 0.00 1.94
381 382 9.764363 TTAAGTAGATGTTTACATAGATGCTGG 57.236 33.333 0.00 0.00 36.57 4.85
382 383 7.603180 AGTAGATGTTTACATAGATGCTGGA 57.397 36.000 0.00 0.00 36.57 3.86
383 384 8.200024 AGTAGATGTTTACATAGATGCTGGAT 57.800 34.615 0.00 0.00 36.57 3.41
384 385 8.654997 AGTAGATGTTTACATAGATGCTGGATT 58.345 33.333 0.00 0.00 36.57 3.01
385 386 9.929180 GTAGATGTTTACATAGATGCTGGATTA 57.071 33.333 0.00 0.00 36.57 1.75
390 391 7.814587 TGTTTACATAGATGCTGGATTATCGAG 59.185 37.037 0.00 0.00 0.00 4.04
417 418 1.264288 CAGGTGAAAGTGCGAAACCTC 59.736 52.381 0.00 0.00 39.24 3.85
429 430 0.161024 GAAACCTCGTGCTTTCGACG 59.839 55.000 0.00 0.00 38.20 5.12
430 431 0.249155 AAACCTCGTGCTTTCGACGA 60.249 50.000 0.00 0.00 43.32 4.20
433 434 2.257371 TCGTGCTTTCGACGAGGG 59.743 61.111 0.00 0.00 40.79 4.30
434 435 2.809601 CGTGCTTTCGACGAGGGG 60.810 66.667 0.00 0.00 39.21 4.79
435 436 2.654877 GTGCTTTCGACGAGGGGA 59.345 61.111 0.00 0.00 0.00 4.81
436 437 1.218316 GTGCTTTCGACGAGGGGAT 59.782 57.895 0.00 0.00 0.00 3.85
437 438 0.391263 GTGCTTTCGACGAGGGGATT 60.391 55.000 0.00 0.00 0.00 3.01
438 439 1.134907 GTGCTTTCGACGAGGGGATTA 60.135 52.381 0.00 0.00 0.00 1.75
439 440 1.760613 TGCTTTCGACGAGGGGATTAT 59.239 47.619 0.00 0.00 0.00 1.28
440 441 2.135933 GCTTTCGACGAGGGGATTATG 58.864 52.381 0.00 0.00 0.00 1.90
441 442 2.223971 GCTTTCGACGAGGGGATTATGA 60.224 50.000 0.00 0.00 0.00 2.15
442 443 3.740141 GCTTTCGACGAGGGGATTATGAA 60.740 47.826 0.00 0.00 0.00 2.57
443 444 3.447918 TTCGACGAGGGGATTATGAAC 57.552 47.619 0.00 0.00 0.00 3.18
444 445 1.684983 TCGACGAGGGGATTATGAACC 59.315 52.381 0.00 0.00 0.00 3.62
445 446 1.687123 CGACGAGGGGATTATGAACCT 59.313 52.381 0.00 0.00 35.67 3.50
463 464 1.199327 CCTGGCATGATGATCATTCGC 59.801 52.381 10.14 12.29 34.28 4.70
528 543 3.503800 AAAGTGTCCCTAAGGTGGAAC 57.496 47.619 0.00 0.00 32.59 3.62
620 636 5.102953 AGTACTCCTAGCATGCAAATTCA 57.897 39.130 21.98 0.00 0.00 2.57
636 652 0.179234 TTCAGGCAGTTCCGTGTCAA 59.821 50.000 0.00 0.00 40.77 3.18
641 657 0.730265 GCAGTTCCGTGTCAACACAA 59.270 50.000 13.30 0.00 46.75 3.33
647 663 0.808453 CCGTGTCAACACAACGAGGT 60.808 55.000 13.30 0.00 46.75 3.85
650 666 1.859080 GTGTCAACACAACGAGGTCTC 59.141 52.381 8.37 0.00 45.75 3.36
651 667 1.754803 TGTCAACACAACGAGGTCTCT 59.245 47.619 0.00 0.00 0.00 3.10
777 793 1.556475 GGTACCCAACCCTCCCTAGTT 60.556 57.143 0.00 0.00 43.16 2.24
843 862 3.181497 CCATCCAGCAATAGAAAACCACG 60.181 47.826 0.00 0.00 0.00 4.94
872 891 1.938861 CACGCACAAAACGCCTAGT 59.061 52.632 0.00 0.00 0.00 2.57
876 895 0.796927 GCACAAAACGCCTAGTCCTC 59.203 55.000 0.00 0.00 0.00 3.71
882 901 2.907917 CGCCTAGTCCTCCCTCCG 60.908 72.222 0.00 0.00 0.00 4.63
934 953 1.805495 CGCACATGCATCTCTAGCTGT 60.805 52.381 0.00 0.00 42.21 4.40
975 994 4.443978 ACAAATATCCATCCAGACCCAG 57.556 45.455 0.00 0.00 0.00 4.45
1188 1213 4.284550 GCCAACCTGCTCCCCACA 62.285 66.667 0.00 0.00 0.00 4.17
1332 1357 0.905357 CCTTCACCGACTCCCTCAAT 59.095 55.000 0.00 0.00 0.00 2.57
1626 1651 3.851845 CTTCGTCGCGTTCCCCACA 62.852 63.158 5.77 0.00 0.00 4.17
1703 1728 7.486870 CACTTGAATAAATTAAACTTACCCGCC 59.513 37.037 0.00 0.00 0.00 6.13
1708 1733 9.673454 GAATAAATTAAACTTACCCGCCTATTG 57.327 33.333 0.00 0.00 0.00 1.90
1714 1739 2.290705 ACTTACCCGCCTATTGCAAAGT 60.291 45.455 1.71 0.00 41.33 2.66
1747 1772 5.499313 ACTCTGGTTACAGTAGTACTCCTC 58.501 45.833 0.00 0.00 45.14 3.71
1800 1825 5.990745 TTTCGATTTCTTGCTTATTTGCG 57.009 34.783 0.00 0.00 35.36 4.85
1814 1839 5.678616 GCTTATTTGCGTGTGGGATGTAAAT 60.679 40.000 0.00 0.00 38.81 1.40
1928 2011 6.078664 TGCCTGGGTCCTAAATCTTTTTAAA 58.921 36.000 0.00 0.00 0.00 1.52
1935 2018 9.135843 GGGTCCTAAATCTTTTTAAATTGTTCG 57.864 33.333 0.00 0.00 0.00 3.95
2035 2121 1.899814 AGGCTGGATAACGACTTGTCA 59.100 47.619 0.00 0.00 0.00 3.58
2078 2164 2.914278 TCGAACCCTAATTCCTTCCCAA 59.086 45.455 0.00 0.00 0.00 4.12
2080 2166 3.632145 CGAACCCTAATTCCTTCCCAATG 59.368 47.826 0.00 0.00 0.00 2.82
2120 2232 0.555769 ACCCCTCTCTGGCAAAACAA 59.444 50.000 0.00 0.00 0.00 2.83
2578 2722 9.211410 CTAGATGATGGACTCCTAATTATGGAT 57.789 37.037 0.00 0.00 32.56 3.41
2625 2769 1.676006 AGCACTTGTTCCAAAGTTCCG 59.324 47.619 0.00 0.00 38.34 4.30
2636 2780 3.504520 TCCAAAGTTCCGGTATTTTCAGC 59.495 43.478 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.660917 GTTCGGGCCCTCTCGATAG 59.339 63.158 22.43 0.54 35.25 2.08
6 7 1.831286 GGTTCGGGCCCTCTCGATA 60.831 63.158 22.43 0.33 35.25 2.92
7 8 3.155167 GGTTCGGGCCCTCTCGAT 61.155 66.667 22.43 0.00 35.25 3.59
8 9 4.377760 AGGTTCGGGCCCTCTCGA 62.378 66.667 22.43 9.26 0.00 4.04
9 10 4.148825 CAGGTTCGGGCCCTCTCG 62.149 72.222 22.43 6.49 0.00 4.04
10 11 3.787001 CCAGGTTCGGGCCCTCTC 61.787 72.222 22.43 9.34 0.00 3.20
18 19 2.160813 CGATGTTTTTACCCAGGTTCGG 59.839 50.000 0.00 0.00 0.00 4.30
19 20 2.809696 ACGATGTTTTTACCCAGGTTCG 59.190 45.455 0.00 0.00 0.00 3.95
20 21 3.566742 ACACGATGTTTTTACCCAGGTTC 59.433 43.478 0.00 0.00 0.00 3.62
21 22 3.558033 ACACGATGTTTTTACCCAGGTT 58.442 40.909 0.00 0.00 0.00 3.50
22 23 3.143728 GACACGATGTTTTTACCCAGGT 58.856 45.455 0.00 0.00 0.00 4.00
23 24 2.486592 GGACACGATGTTTTTACCCAGG 59.513 50.000 0.00 0.00 0.00 4.45
24 25 2.486592 GGGACACGATGTTTTTACCCAG 59.513 50.000 0.00 0.00 31.68 4.45
25 26 2.106857 AGGGACACGATGTTTTTACCCA 59.893 45.455 0.00 0.00 33.25 4.51
26 27 2.786777 AGGGACACGATGTTTTTACCC 58.213 47.619 0.00 0.00 31.54 3.69
27 28 3.566742 ACAAGGGACACGATGTTTTTACC 59.433 43.478 0.00 0.00 0.00 2.85
28 29 4.514066 AGACAAGGGACACGATGTTTTTAC 59.486 41.667 0.00 0.00 0.00 2.01
29 30 4.710324 AGACAAGGGACACGATGTTTTTA 58.290 39.130 0.00 0.00 0.00 1.52
30 31 3.551846 AGACAAGGGACACGATGTTTTT 58.448 40.909 0.00 0.00 0.00 1.94
31 32 3.139077 GAGACAAGGGACACGATGTTTT 58.861 45.455 0.00 0.00 0.00 2.43
32 33 2.550208 GGAGACAAGGGACACGATGTTT 60.550 50.000 0.00 0.00 0.00 2.83
33 34 1.002087 GGAGACAAGGGACACGATGTT 59.998 52.381 0.00 0.00 0.00 2.71
34 35 0.608640 GGAGACAAGGGACACGATGT 59.391 55.000 0.00 0.00 0.00 3.06
35 36 0.898320 AGGAGACAAGGGACACGATG 59.102 55.000 0.00 0.00 0.00 3.84
36 37 0.898320 CAGGAGACAAGGGACACGAT 59.102 55.000 0.00 0.00 0.00 3.73
37 38 0.469331 ACAGGAGACAAGGGACACGA 60.469 55.000 0.00 0.00 0.00 4.35
38 39 0.393077 AACAGGAGACAAGGGACACG 59.607 55.000 0.00 0.00 0.00 4.49
39 40 2.289506 GGTAACAGGAGACAAGGGACAC 60.290 54.545 0.00 0.00 0.00 3.67
40 41 1.975680 GGTAACAGGAGACAAGGGACA 59.024 52.381 0.00 0.00 0.00 4.02
41 42 1.975680 TGGTAACAGGAGACAAGGGAC 59.024 52.381 0.00 0.00 46.17 4.46
42 43 2.409064 TGGTAACAGGAGACAAGGGA 57.591 50.000 0.00 0.00 46.17 4.20
55 56 0.596859 GCGTCTAGGCGGATGGTAAC 60.597 60.000 19.86 0.00 0.00 2.50
56 57 1.038681 TGCGTCTAGGCGGATGGTAA 61.039 55.000 19.86 0.00 35.06 2.85
57 58 1.454295 TGCGTCTAGGCGGATGGTA 60.454 57.895 19.86 0.00 35.06 3.25
58 59 2.758327 TGCGTCTAGGCGGATGGT 60.758 61.111 19.86 0.00 35.06 3.55
59 60 2.279517 GTGCGTCTAGGCGGATGG 60.280 66.667 19.86 0.00 34.24 3.51
60 61 1.589993 CTGTGCGTCTAGGCGGATG 60.590 63.158 19.86 9.25 34.24 3.51
61 62 1.605058 AACTGTGCGTCTAGGCGGAT 61.605 55.000 19.86 0.00 34.24 4.18
62 63 2.209064 GAACTGTGCGTCTAGGCGGA 62.209 60.000 19.86 14.02 35.06 5.54
63 64 1.805945 GAACTGTGCGTCTAGGCGG 60.806 63.158 19.86 3.85 35.06 6.13
64 65 2.152699 CGAACTGTGCGTCTAGGCG 61.153 63.158 13.55 13.55 35.06 5.52
65 66 1.805945 CCGAACTGTGCGTCTAGGC 60.806 63.158 7.51 0.00 0.00 3.93
66 67 1.153823 CCCGAACTGTGCGTCTAGG 60.154 63.158 7.51 0.00 0.00 3.02
67 68 0.456312 GTCCCGAACTGTGCGTCTAG 60.456 60.000 7.51 0.00 0.00 2.43
68 69 1.582968 GTCCCGAACTGTGCGTCTA 59.417 57.895 7.51 0.00 0.00 2.59
69 70 2.338984 GTCCCGAACTGTGCGTCT 59.661 61.111 7.51 0.00 0.00 4.18
70 71 2.737376 GGTCCCGAACTGTGCGTC 60.737 66.667 7.51 0.00 0.00 5.19
71 72 4.309950 GGGTCCCGAACTGTGCGT 62.310 66.667 7.51 0.00 0.00 5.24
73 74 4.717313 GGGGGTCCCGAACTGTGC 62.717 72.222 0.48 0.00 36.85 4.57
82 83 3.097429 ATCTCGGGTAGGGGGTCCC 62.097 68.421 0.00 0.00 45.90 4.46
83 84 1.533513 GATCTCGGGTAGGGGGTCC 60.534 68.421 0.00 0.00 0.00 4.46
84 85 1.533513 GGATCTCGGGTAGGGGGTC 60.534 68.421 0.00 0.00 0.00 4.46
85 86 2.613421 GGATCTCGGGTAGGGGGT 59.387 66.667 0.00 0.00 0.00 4.95
86 87 2.600769 CGGATCTCGGGTAGGGGG 60.601 72.222 0.00 0.00 34.75 5.40
87 88 3.303928 GCGGATCTCGGGTAGGGG 61.304 72.222 5.87 0.00 39.69 4.79
88 89 3.303928 GGCGGATCTCGGGTAGGG 61.304 72.222 5.87 0.00 39.69 3.53
89 90 3.671411 CGGCGGATCTCGGGTAGG 61.671 72.222 0.00 0.00 39.69 3.18
90 91 3.671411 CCGGCGGATCTCGGGTAG 61.671 72.222 24.41 0.00 42.32 3.18
95 96 1.447140 TCAAAACCGGCGGATCTCG 60.447 57.895 35.78 16.34 42.76 4.04
96 97 0.672401 TGTCAAAACCGGCGGATCTC 60.672 55.000 35.78 16.90 0.00 2.75
97 98 0.953960 GTGTCAAAACCGGCGGATCT 60.954 55.000 35.78 13.84 0.00 2.75
98 99 1.500396 GTGTCAAAACCGGCGGATC 59.500 57.895 35.78 9.52 0.00 3.36
99 100 1.969589 GGTGTCAAAACCGGCGGAT 60.970 57.895 35.78 20.37 0.00 4.18
100 101 2.592287 GGTGTCAAAACCGGCGGA 60.592 61.111 35.78 6.54 0.00 5.54
106 107 3.001939 CAGTTAGTGTCGGTGTCAAAACC 59.998 47.826 0.00 0.00 36.82 3.27
107 108 3.619929 ACAGTTAGTGTCGGTGTCAAAAC 59.380 43.478 0.00 0.00 31.90 2.43
108 109 3.619483 CACAGTTAGTGTCGGTGTCAAAA 59.381 43.478 0.00 0.00 43.40 2.44
109 110 3.191669 CACAGTTAGTGTCGGTGTCAAA 58.808 45.455 0.00 0.00 43.40 2.69
110 111 2.816689 CACAGTTAGTGTCGGTGTCAA 58.183 47.619 0.00 0.00 43.40 3.18
111 112 2.502213 CACAGTTAGTGTCGGTGTCA 57.498 50.000 0.00 0.00 43.40 3.58
121 122 0.466543 TCCACAACGGCACAGTTAGT 59.533 50.000 0.00 0.00 32.35 2.24
122 123 1.148310 CTCCACAACGGCACAGTTAG 58.852 55.000 0.00 0.00 32.35 2.34
123 124 0.250124 CCTCCACAACGGCACAGTTA 60.250 55.000 0.00 0.00 32.35 2.24
124 125 1.525995 CCTCCACAACGGCACAGTT 60.526 57.895 0.00 0.00 34.15 3.16
125 126 1.768684 ATCCTCCACAACGGCACAGT 61.769 55.000 0.00 0.00 33.14 3.55
126 127 0.606401 AATCCTCCACAACGGCACAG 60.606 55.000 0.00 0.00 33.14 3.66
127 128 0.605319 GAATCCTCCACAACGGCACA 60.605 55.000 0.00 0.00 33.14 4.57
128 129 0.321653 AGAATCCTCCACAACGGCAC 60.322 55.000 0.00 0.00 33.14 5.01
129 130 0.036388 GAGAATCCTCCACAACGGCA 60.036 55.000 0.00 0.00 33.30 5.69
130 131 0.250513 AGAGAATCCTCCACAACGGC 59.749 55.000 0.00 0.00 40.30 5.68
131 132 2.301577 GAGAGAATCCTCCACAACGG 57.698 55.000 0.00 0.00 40.30 4.44
142 143 0.179097 GCGAGTGGGTGGAGAGAATC 60.179 60.000 0.00 0.00 0.00 2.52
143 144 0.904865 TGCGAGTGGGTGGAGAGAAT 60.905 55.000 0.00 0.00 0.00 2.40
144 145 1.533033 TGCGAGTGGGTGGAGAGAA 60.533 57.895 0.00 0.00 0.00 2.87
145 146 2.117423 TGCGAGTGGGTGGAGAGA 59.883 61.111 0.00 0.00 0.00 3.10
146 147 2.262915 GTGCGAGTGGGTGGAGAG 59.737 66.667 0.00 0.00 0.00 3.20
147 148 3.311110 GGTGCGAGTGGGTGGAGA 61.311 66.667 0.00 0.00 0.00 3.71
148 149 2.469465 AATGGTGCGAGTGGGTGGAG 62.469 60.000 0.00 0.00 0.00 3.86
149 150 2.063015 AAATGGTGCGAGTGGGTGGA 62.063 55.000 0.00 0.00 0.00 4.02
150 151 1.603455 AAATGGTGCGAGTGGGTGG 60.603 57.895 0.00 0.00 0.00 4.61
151 152 1.580942 CAAATGGTGCGAGTGGGTG 59.419 57.895 0.00 0.00 0.00 4.61
152 153 1.603455 CCAAATGGTGCGAGTGGGT 60.603 57.895 0.00 0.00 0.00 4.51
153 154 2.342650 CCCAAATGGTGCGAGTGGG 61.343 63.158 0.00 0.00 42.94 4.61
154 155 2.342650 CCCCAAATGGTGCGAGTGG 61.343 63.158 0.00 0.00 0.00 4.00
155 156 1.178534 AACCCCAAATGGTGCGAGTG 61.179 55.000 0.00 0.00 39.05 3.51
156 157 1.152830 AACCCCAAATGGTGCGAGT 59.847 52.632 0.00 0.00 39.05 4.18
157 158 0.893270 TCAACCCCAAATGGTGCGAG 60.893 55.000 0.00 0.00 39.05 5.03
158 159 0.468214 TTCAACCCCAAATGGTGCGA 60.468 50.000 0.00 0.00 39.05 5.10
159 160 0.319469 GTTCAACCCCAAATGGTGCG 60.319 55.000 0.00 0.00 39.05 5.34
160 161 0.034756 GGTTCAACCCCAAATGGTGC 59.965 55.000 0.00 0.00 39.05 5.01
171 172 4.142160 GCCATAAAATGAGAGGGTTCAACC 60.142 45.833 0.00 0.00 37.60 3.77
172 173 4.462483 TGCCATAAAATGAGAGGGTTCAAC 59.538 41.667 0.00 0.00 0.00 3.18
173 174 4.671831 TGCCATAAAATGAGAGGGTTCAA 58.328 39.130 0.00 0.00 0.00 2.69
174 175 4.314522 TGCCATAAAATGAGAGGGTTCA 57.685 40.909 0.00 0.00 0.00 3.18
175 176 5.360714 TGAATGCCATAAAATGAGAGGGTTC 59.639 40.000 0.00 0.00 0.00 3.62
176 177 5.271598 TGAATGCCATAAAATGAGAGGGTT 58.728 37.500 0.00 0.00 0.00 4.11
177 178 4.870636 TGAATGCCATAAAATGAGAGGGT 58.129 39.130 0.00 0.00 0.00 4.34
178 179 5.738208 GCTTGAATGCCATAAAATGAGAGGG 60.738 44.000 0.00 0.00 0.00 4.30
179 180 5.163488 TGCTTGAATGCCATAAAATGAGAGG 60.163 40.000 0.00 0.00 0.00 3.69
180 181 5.898174 TGCTTGAATGCCATAAAATGAGAG 58.102 37.500 0.00 0.00 0.00 3.20
181 182 5.918426 TGCTTGAATGCCATAAAATGAGA 57.082 34.783 0.00 0.00 0.00 3.27
182 183 6.971527 TTTGCTTGAATGCCATAAAATGAG 57.028 33.333 0.00 0.00 0.00 2.90
183 184 7.741027 TTTTTGCTTGAATGCCATAAAATGA 57.259 28.000 0.00 0.00 0.00 2.57
205 206 8.448615 GCTTACGATAAGGTTAACTGTGATTTT 58.551 33.333 5.42 0.00 0.00 1.82
206 207 7.065443 GGCTTACGATAAGGTTAACTGTGATTT 59.935 37.037 5.42 0.00 0.00 2.17
207 208 6.537660 GGCTTACGATAAGGTTAACTGTGATT 59.462 38.462 5.42 0.00 0.00 2.57
208 209 6.047231 GGCTTACGATAAGGTTAACTGTGAT 58.953 40.000 5.42 0.00 0.00 3.06
209 210 5.186409 AGGCTTACGATAAGGTTAACTGTGA 59.814 40.000 5.42 0.00 0.00 3.58
210 211 5.416947 AGGCTTACGATAAGGTTAACTGTG 58.583 41.667 5.42 0.00 0.00 3.66
211 212 5.672421 AGGCTTACGATAAGGTTAACTGT 57.328 39.130 5.42 0.00 0.00 3.55
212 213 6.338937 AGAAGGCTTACGATAAGGTTAACTG 58.661 40.000 0.00 0.00 0.00 3.16
213 214 6.541934 AGAAGGCTTACGATAAGGTTAACT 57.458 37.500 0.00 0.00 0.00 2.24
214 215 6.815142 TCAAGAAGGCTTACGATAAGGTTAAC 59.185 38.462 0.00 0.00 31.81 2.01
215 216 6.938507 TCAAGAAGGCTTACGATAAGGTTAA 58.061 36.000 0.00 0.00 31.81 2.01
216 217 6.534475 TCAAGAAGGCTTACGATAAGGTTA 57.466 37.500 0.00 0.00 31.81 2.85
217 218 5.416271 TCAAGAAGGCTTACGATAAGGTT 57.584 39.130 0.00 0.00 31.81 3.50
218 219 5.046520 ACTTCAAGAAGGCTTACGATAAGGT 60.047 40.000 13.83 0.00 42.53 3.50
219 220 5.420409 ACTTCAAGAAGGCTTACGATAAGG 58.580 41.667 13.83 0.00 42.53 2.69
220 221 6.100004 TGACTTCAAGAAGGCTTACGATAAG 58.900 40.000 16.07 3.69 46.52 1.73
221 222 6.032956 TGACTTCAAGAAGGCTTACGATAA 57.967 37.500 16.07 0.00 46.52 1.75
222 223 5.654603 TGACTTCAAGAAGGCTTACGATA 57.345 39.130 16.07 0.00 46.52 2.92
223 224 4.537135 TGACTTCAAGAAGGCTTACGAT 57.463 40.909 16.07 0.00 46.52 3.73
224 225 4.330944 TTGACTTCAAGAAGGCTTACGA 57.669 40.909 16.07 0.00 46.52 3.43
236 237 6.329496 GGATTGTGTTGAAACTTGACTTCAA 58.671 36.000 0.00 0.00 39.79 2.69
237 238 5.163561 GGGATTGTGTTGAAACTTGACTTCA 60.164 40.000 0.00 0.00 0.00 3.02
238 239 5.281727 GGGATTGTGTTGAAACTTGACTTC 58.718 41.667 0.00 0.00 0.00 3.01
239 240 4.099419 GGGGATTGTGTTGAAACTTGACTT 59.901 41.667 0.00 0.00 0.00 3.01
240 241 3.636764 GGGGATTGTGTTGAAACTTGACT 59.363 43.478 0.00 0.00 0.00 3.41
241 242 3.550030 CGGGGATTGTGTTGAAACTTGAC 60.550 47.826 0.00 0.00 0.00 3.18
242 243 2.621055 CGGGGATTGTGTTGAAACTTGA 59.379 45.455 0.00 0.00 0.00 3.02
243 244 2.862140 GCGGGGATTGTGTTGAAACTTG 60.862 50.000 0.00 0.00 0.00 3.16
244 245 1.339929 GCGGGGATTGTGTTGAAACTT 59.660 47.619 0.00 0.00 0.00 2.66
245 246 0.958822 GCGGGGATTGTGTTGAAACT 59.041 50.000 0.00 0.00 0.00 2.66
246 247 0.958822 AGCGGGGATTGTGTTGAAAC 59.041 50.000 0.00 0.00 0.00 2.78
247 248 1.698506 AAGCGGGGATTGTGTTGAAA 58.301 45.000 0.00 0.00 0.00 2.69
248 249 1.698506 AAAGCGGGGATTGTGTTGAA 58.301 45.000 0.00 0.00 0.00 2.69
249 250 1.698506 AAAAGCGGGGATTGTGTTGA 58.301 45.000 0.00 0.00 0.00 3.18
250 251 2.524569 AAAAAGCGGGGATTGTGTTG 57.475 45.000 0.00 0.00 0.00 3.33
266 267 5.885352 TCCATCACACTCAAGTCAAGAAAAA 59.115 36.000 0.00 0.00 0.00 1.94
267 268 5.436175 TCCATCACACTCAAGTCAAGAAAA 58.564 37.500 0.00 0.00 0.00 2.29
268 269 5.034852 TCCATCACACTCAAGTCAAGAAA 57.965 39.130 0.00 0.00 0.00 2.52
269 270 4.503817 CCTCCATCACACTCAAGTCAAGAA 60.504 45.833 0.00 0.00 0.00 2.52
270 271 3.007290 CCTCCATCACACTCAAGTCAAGA 59.993 47.826 0.00 0.00 0.00 3.02
271 272 3.007290 TCCTCCATCACACTCAAGTCAAG 59.993 47.826 0.00 0.00 0.00 3.02
272 273 2.972021 TCCTCCATCACACTCAAGTCAA 59.028 45.455 0.00 0.00 0.00 3.18
273 274 2.608623 TCCTCCATCACACTCAAGTCA 58.391 47.619 0.00 0.00 0.00 3.41
274 275 3.902881 ATCCTCCATCACACTCAAGTC 57.097 47.619 0.00 0.00 0.00 3.01
275 276 4.042062 TGAAATCCTCCATCACACTCAAGT 59.958 41.667 0.00 0.00 0.00 3.16
276 277 4.582869 TGAAATCCTCCATCACACTCAAG 58.417 43.478 0.00 0.00 0.00 3.02
277 278 4.639078 TGAAATCCTCCATCACACTCAA 57.361 40.909 0.00 0.00 0.00 3.02
278 279 4.520179 CATGAAATCCTCCATCACACTCA 58.480 43.478 0.00 0.00 0.00 3.41
279 280 3.314635 GCATGAAATCCTCCATCACACTC 59.685 47.826 0.00 0.00 0.00 3.51
280 281 3.285484 GCATGAAATCCTCCATCACACT 58.715 45.455 0.00 0.00 0.00 3.55
281 282 3.018856 TGCATGAAATCCTCCATCACAC 58.981 45.455 0.00 0.00 0.00 3.82
282 283 3.369242 TGCATGAAATCCTCCATCACA 57.631 42.857 0.00 0.00 0.00 3.58
283 284 3.067742 CCTTGCATGAAATCCTCCATCAC 59.932 47.826 0.00 0.00 0.00 3.06
284 285 3.293337 CCTTGCATGAAATCCTCCATCA 58.707 45.455 0.00 0.00 0.00 3.07
285 286 3.294214 ACCTTGCATGAAATCCTCCATC 58.706 45.455 0.00 0.00 0.00 3.51
286 287 3.294214 GACCTTGCATGAAATCCTCCAT 58.706 45.455 0.00 0.00 0.00 3.41
287 288 2.041485 TGACCTTGCATGAAATCCTCCA 59.959 45.455 0.00 0.00 0.00 3.86
288 289 2.726821 TGACCTTGCATGAAATCCTCC 58.273 47.619 0.00 0.00 0.00 4.30
289 290 4.012374 TCTTGACCTTGCATGAAATCCTC 58.988 43.478 0.00 0.00 0.00 3.71
290 291 4.038271 TCTTGACCTTGCATGAAATCCT 57.962 40.909 0.00 0.00 0.00 3.24
291 292 4.996788 ATCTTGACCTTGCATGAAATCC 57.003 40.909 0.00 0.00 0.00 3.01
292 293 5.105635 TGGAATCTTGACCTTGCATGAAATC 60.106 40.000 0.00 0.00 0.00 2.17
293 294 4.773674 TGGAATCTTGACCTTGCATGAAAT 59.226 37.500 0.00 0.00 0.00 2.17
294 295 4.151121 TGGAATCTTGACCTTGCATGAAA 58.849 39.130 0.00 0.00 0.00 2.69
295 296 3.765381 TGGAATCTTGACCTTGCATGAA 58.235 40.909 0.00 0.00 0.00 2.57
296 297 3.438216 TGGAATCTTGACCTTGCATGA 57.562 42.857 0.00 0.00 0.00 3.07
297 298 3.067742 GGATGGAATCTTGACCTTGCATG 59.932 47.826 0.00 0.00 44.71 4.06
298 299 3.294214 GGATGGAATCTTGACCTTGCAT 58.706 45.455 0.00 0.00 44.71 3.96
299 300 2.041485 TGGATGGAATCTTGACCTTGCA 59.959 45.455 0.00 0.00 44.71 4.08
300 301 2.726821 TGGATGGAATCTTGACCTTGC 58.273 47.619 0.00 0.00 44.71 4.01
301 302 7.592885 AATTATGGATGGAATCTTGACCTTG 57.407 36.000 0.00 0.00 44.71 3.61
302 303 8.613922 AAAATTATGGATGGAATCTTGACCTT 57.386 30.769 0.00 0.00 44.71 3.50
303 304 8.480501 CAAAAATTATGGATGGAATCTTGACCT 58.519 33.333 0.00 0.00 44.71 3.85
304 305 8.477256 TCAAAAATTATGGATGGAATCTTGACC 58.523 33.333 0.00 0.00 44.71 4.02
305 306 9.874205 TTCAAAAATTATGGATGGAATCTTGAC 57.126 29.630 0.00 0.00 44.71 3.18
355 356 9.764363 CCAGCATCTATGTAAACATCTACTTAA 57.236 33.333 0.00 0.00 37.76 1.85
369 370 6.596309 TTCTCGATAATCCAGCATCTATGT 57.404 37.500 0.00 0.00 0.00 2.29
370 371 7.601886 AGTTTTCTCGATAATCCAGCATCTATG 59.398 37.037 0.00 0.00 0.00 2.23
372 373 7.055667 AGTTTTCTCGATAATCCAGCATCTA 57.944 36.000 0.00 0.00 0.00 1.98
373 374 5.923204 AGTTTTCTCGATAATCCAGCATCT 58.077 37.500 0.00 0.00 0.00 2.90
374 375 6.221858 GAGTTTTCTCGATAATCCAGCATC 57.778 41.667 0.00 0.00 37.19 3.91
390 391 2.612212 TCGCACTTTCACCTGAGTTTTC 59.388 45.455 0.00 0.00 0.00 2.29
417 418 2.558554 ATCCCCTCGTCGAAAGCACG 62.559 60.000 0.00 0.00 36.47 5.34
425 426 1.687123 AGGTTCATAATCCCCTCGTCG 59.313 52.381 0.00 0.00 0.00 5.12
426 427 2.224305 CCAGGTTCATAATCCCCTCGTC 60.224 54.545 0.00 0.00 0.00 4.20
427 428 1.768870 CCAGGTTCATAATCCCCTCGT 59.231 52.381 0.00 0.00 0.00 4.18
428 429 1.543429 GCCAGGTTCATAATCCCCTCG 60.543 57.143 0.00 0.00 0.00 4.63
429 430 1.494721 TGCCAGGTTCATAATCCCCTC 59.505 52.381 0.00 0.00 0.00 4.30
430 431 1.607225 TGCCAGGTTCATAATCCCCT 58.393 50.000 0.00 0.00 0.00 4.79
431 432 2.158475 TCATGCCAGGTTCATAATCCCC 60.158 50.000 0.00 0.00 0.00 4.81
432 433 3.228188 TCATGCCAGGTTCATAATCCC 57.772 47.619 0.00 0.00 0.00 3.85
433 434 4.401022 TCATCATGCCAGGTTCATAATCC 58.599 43.478 0.00 0.00 0.00 3.01
434 435 5.708697 TGATCATCATGCCAGGTTCATAATC 59.291 40.000 0.00 0.00 0.00 1.75
435 436 5.637127 TGATCATCATGCCAGGTTCATAAT 58.363 37.500 0.00 0.00 0.00 1.28
436 437 5.051409 TGATCATCATGCCAGGTTCATAA 57.949 39.130 0.00 0.00 0.00 1.90
437 438 4.710313 TGATCATCATGCCAGGTTCATA 57.290 40.909 0.00 0.00 0.00 2.15
438 439 3.588210 TGATCATCATGCCAGGTTCAT 57.412 42.857 0.00 0.00 0.00 2.57
439 440 3.588210 ATGATCATCATGCCAGGTTCA 57.412 42.857 1.18 0.00 35.43 3.18
440 441 3.058432 CGAATGATCATCATGCCAGGTTC 60.058 47.826 9.06 0.00 37.15 3.62
441 442 2.882761 CGAATGATCATCATGCCAGGTT 59.117 45.455 9.06 0.00 37.15 3.50
442 443 2.501261 CGAATGATCATCATGCCAGGT 58.499 47.619 9.06 0.00 37.15 4.00
443 444 1.199327 GCGAATGATCATCATGCCAGG 59.801 52.381 9.06 0.00 37.15 4.45
444 445 1.199327 GGCGAATGATCATCATGCCAG 59.801 52.381 27.77 6.00 42.35 4.85
445 446 1.241165 GGCGAATGATCATCATGCCA 58.759 50.000 27.77 0.00 42.35 4.92
463 464 1.821216 AGATAAAACCCACACGCTGG 58.179 50.000 0.00 0.00 40.26 4.85
475 476 3.655486 TCGACGTGGAGCAAAGATAAAA 58.345 40.909 0.00 0.00 0.00 1.52
522 537 2.437413 GATCAGTTTGGGAGGTTCCAC 58.563 52.381 0.00 0.00 38.64 4.02
528 543 1.630369 TCACTGGATCAGTTTGGGAGG 59.370 52.381 0.00 0.00 42.59 4.30
620 636 0.814010 GTGTTGACACGGAACTGCCT 60.814 55.000 0.00 0.00 37.10 4.75
636 652 1.186267 GGGGAGAGACCTCGTTGTGT 61.186 60.000 0.00 0.00 40.33 3.72
647 663 0.340208 GGAAGAAGGGAGGGGAGAGA 59.660 60.000 0.00 0.00 0.00 3.10
650 666 0.692756 GAGGGAAGAAGGGAGGGGAG 60.693 65.000 0.00 0.00 0.00 4.30
651 667 1.396594 GAGGGAAGAAGGGAGGGGA 59.603 63.158 0.00 0.00 0.00 4.81
777 793 1.003355 GCTTAGGCTGGCAGTGTCA 60.003 57.895 17.16 0.00 35.22 3.58
872 891 1.007238 AGATTCTTGACGGAGGGAGGA 59.993 52.381 0.00 0.00 0.00 3.71
876 895 3.489398 CGTAGAAGATTCTTGACGGAGGG 60.489 52.174 17.01 0.00 36.27 4.30
882 901 3.243336 ACGTGCGTAGAAGATTCTTGAC 58.757 45.455 3.03 1.17 38.70 3.18
971 990 0.888736 TTGTGCGTGATTGGACTGGG 60.889 55.000 0.00 0.00 0.00 4.45
975 994 2.584791 GATTGTTGTGCGTGATTGGAC 58.415 47.619 0.00 0.00 0.00 4.02
1188 1213 1.003718 GAAAGCCAGCACCGTACCT 60.004 57.895 0.00 0.00 0.00 3.08
1191 1216 3.152865 TGGAAAGCCAGCACCGTA 58.847 55.556 0.00 0.00 39.92 4.02
1494 1519 1.004440 GTTCTTGTCTCTGGCCGCT 60.004 57.895 0.00 0.00 0.00 5.52
1680 1705 7.706100 AGGCGGGTAAGTTTAATTTATTCAA 57.294 32.000 0.00 0.00 0.00 2.69
1703 1728 9.552114 CAGAGTAATTCTTGAACTTTGCAATAG 57.448 33.333 0.00 3.50 32.41 1.73
1708 1733 6.319141 ACCAGAGTAATTCTTGAACTTTGC 57.681 37.500 0.00 0.00 32.41 3.68
1714 1739 8.867097 ACTACTGTAACCAGAGTAATTCTTGAA 58.133 33.333 0.00 0.00 41.50 2.69
1747 1772 9.553064 AGAATGATACAATGCTCTTAAGTTAGG 57.447 33.333 1.63 0.00 0.00 2.69
1800 1825 3.560068 GTCGGATCATTTACATCCCACAC 59.440 47.826 0.00 0.00 37.14 3.82
1814 1839 6.996282 TGTGTGTAGAATCTATAGTCGGATCA 59.004 38.462 0.00 0.00 0.00 2.92
1928 2011 1.843368 TAGGACCTCGGACGAACAAT 58.157 50.000 0.00 0.00 0.00 2.71
1935 2018 2.037381 GGATGGAATTAGGACCTCGGAC 59.963 54.545 0.00 0.00 0.00 4.79
1996 2079 3.311110 GGCCTCCAGTCCACGTGA 61.311 66.667 19.30 0.00 0.00 4.35
2035 2121 5.760253 CGAGGGTTCTTTTGCAGATATGTAT 59.240 40.000 0.00 0.00 0.00 2.29
2078 2164 2.998949 GGAGGAAAGGACCGCCAT 59.001 61.111 0.00 0.00 46.63 4.40
2225 2341 4.294702 ACCATATAGCAGAGGAGGATCTCT 59.705 45.833 0.00 0.00 44.25 3.10
2241 2357 2.366266 GGTTACGGGCACTGACCATATA 59.634 50.000 0.64 0.00 38.67 0.86
2292 2422 3.312736 ACCATGGATTCGGCCTAAATT 57.687 42.857 21.47 0.00 0.00 1.82
2391 2522 1.156736 CTTCGACTTGCCAAATCCGT 58.843 50.000 0.00 0.00 0.00 4.69
2569 2713 6.003326 TGTGTCAGTGTCACAATCCATAATT 58.997 36.000 18.90 0.00 41.83 1.40
2578 2722 2.097304 GTGCAATGTGTCAGTGTCACAA 59.903 45.455 23.65 7.72 46.47 3.33
2625 2769 5.417580 TGGTCCATAAACAGCTGAAAATACC 59.582 40.000 23.35 17.42 0.00 2.73
2636 2780 7.336679 TGTCATATCTTTGTGGTCCATAAACAG 59.663 37.037 9.56 2.14 0.00 3.16


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

AutoCloner maintained by Alex Coulton.