Multiple sequence alignment - TraesCS2A01G012900

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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 TraesCS2A01G012900 chr2A 100.000 5761 0 0 1 5761 4983104 4977344 0.000000e+00 10639.0
1 TraesCS2A01G012900 chr2B 91.941 5137 277 52 205 5233 3288093 3293200 0.000000e+00 7066.0
2 TraesCS2A01G012900 chr2B 92.647 136 10 0 27 162 371162765 371162630 4.550000e-46 196.0
3 TraesCS2A01G012900 chr2B 89.844 128 13 0 30 157 150604691 150604818 1.280000e-36 165.0
4 TraesCS2A01G012900 chr2B 90.000 60 6 0 4240 4299 66560806 66560865 1.720000e-10 78.7
5 TraesCS2A01G012900 chr2D 93.903 3395 152 22 639 3988 6704423 6707807 0.000000e+00 5072.0
6 TraesCS2A01G012900 chr2D 92.034 1180 47 20 4011 5160 6708014 6709176 0.000000e+00 1615.0
7 TraesCS2A01G012900 chr2D 97.010 602 18 0 5160 5761 6709205 6709806 0.000000e+00 1013.0
8 TraesCS2A01G012900 chr2D 91.477 176 11 1 238 409 6703890 6704065 7.460000e-59 239.0
9 TraesCS2A01G012900 chr2D 80.851 282 21 17 4903 5160 6925932 6926204 2.120000e-44 191.0
10 TraesCS2A01G012900 chr2D 89.051 137 15 0 28 164 429922140 429922276 2.760000e-38 171.0
11 TraesCS2A01G012900 chr2D 97.297 74 2 0 574 647 6704198 6704271 6.060000e-25 126.0
12 TraesCS2A01G012900 chr2D 91.667 60 5 0 4240 4299 38095024 38095083 3.700000e-12 84.2
13 TraesCS2A01G012900 chr2D 100.000 28 0 0 4114 4141 552542500 552542473 1.000000e-02 52.8
14 TraesCS2A01G012900 chr4D 83.926 2476 319 42 1511 3962 2955440 2957860 0.000000e+00 2294.0
15 TraesCS2A01G012900 chr4D 88.028 142 15 1 28 169 54796551 54796412 3.570000e-37 167.0
16 TraesCS2A01G012900 chrUn 82.115 2270 327 39 1726 3962 47833830 47831607 0.000000e+00 1869.0
17 TraesCS2A01G012900 chr7B 75.303 413 79 17 3560 3962 713041746 713042145 5.930000e-40 176.0
18 TraesCS2A01G012900 chr7B 84.615 104 12 4 4214 4315 480694782 480694883 3.670000e-17 100.0
19 TraesCS2A01G012900 chr1A 89.286 140 14 1 29 167 285990846 285990985 2.130000e-39 174.0
20 TraesCS2A01G012900 chr5D 89.130 138 13 1 26 163 23153855 23153990 2.760000e-38 171.0
21 TraesCS2A01G012900 chr5D 95.556 45 2 0 4240 4284 327524447 327524491 8.010000e-09 73.1
22 TraesCS2A01G012900 chr7A 74.576 413 86 16 3559 3963 712180062 712180463 4.620000e-36 163.0
23 TraesCS2A01G012900 chr4A 88.148 135 16 0 30 164 114583324 114583190 1.660000e-35 161.0
24 TraesCS2A01G012900 chr6D 89.062 128 14 0 30 157 117041019 117041146 5.970000e-35 159.0
25 TraesCS2A01G012900 chr7D 74.402 418 84 16 3559 3963 618488500 618488907 2.150000e-34 158.0
26 TraesCS2A01G012900 chr7D 84.615 104 12 4 4214 4315 458726696 458726797 3.670000e-17 100.0
27 TraesCS2A01G012900 chr1B 86.525 141 17 1 26 166 646540019 646539881 2.780000e-33 154.0
28 TraesCS2A01G012900 chr5B 95.556 45 2 0 4240 4284 380817069 380817113 8.010000e-09 73.1
29 TraesCS2A01G012900 chr5A 88.333 60 7 0 4240 4299 429170109 429170050 8.010000e-09 73.1
30 TraesCS2A01G012900 chr3A 85.507 69 8 2 4094 4160 710784379 710784311 2.880000e-08 71.3


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 TraesCS2A01G012900 chr2A 4977344 4983104 5760 True 10639 10639 100.0000 1 5761 1 chr2A.!!$R1 5760
1 TraesCS2A01G012900 chr2B 3288093 3293200 5107 False 7066 7066 91.9410 205 5233 1 chr2B.!!$F1 5028
2 TraesCS2A01G012900 chr2D 6703890 6709806 5916 False 1613 5072 94.3442 238 5761 5 chr2D.!!$F4 5523
3 TraesCS2A01G012900 chr4D 2955440 2957860 2420 False 2294 2294 83.9260 1511 3962 1 chr4D.!!$F1 2451
4 TraesCS2A01G012900 chrUn 47831607 47833830 2223 True 1869 1869 82.1150 1726 3962 1 chrUn.!!$R1 2236

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
170 171 0.036306 ACAGGGTCTAAGTTTGCCGG 59.964 55.000 0.00 0.00 0.00 6.13 F
203 204 0.111446 TTCGTGGGCATTTTCTGGGA 59.889 50.000 0.00 0.00 0.00 4.37 F
902 1156 0.457035 GAGAGTGAGAGCTGCCTCAG 59.543 60.000 17.37 0.00 43.15 3.35 F
1167 1441 0.758123 CCTTCCTCTCCTCATGGCTC 59.242 60.000 0.00 0.00 0.00 4.70 F
2673 2955 0.178068 ACGTCTCACACAACCAGCTT 59.822 50.000 0.00 0.00 0.00 3.74 F
3396 3681 1.216710 GGTGAGCTTCTCCGTGGAG 59.783 63.158 9.73 9.73 43.21 3.86 F
3612 3897 1.793613 GCACAAGAACATCGTGCGC 60.794 57.895 0.00 0.00 45.69 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 1945 0.036765 TGGAAAACGAGTCGGGGATG 60.037 55.000 18.30 0.00 0.00 3.51 R
1686 1960 0.321671 CGAGGTTGGAGAGCTTGGAA 59.678 55.000 0.00 0.00 35.91 3.53 R
1986 2260 1.634225 GTCGAGCGAGACGAGAGAG 59.366 63.158 0.00 0.00 40.37 3.20 R
2994 3276 0.469331 TGAGGGTGACGAGGTTGTCT 60.469 55.000 0.00 0.00 39.64 3.41 R
3988 4294 0.603569 GAGTCATATCGGACCGGCAT 59.396 55.000 15.25 3.44 38.59 4.40 R
4409 4920 0.908198 GCAACATCTCCTCCACCTCT 59.092 55.000 0.00 0.00 0.00 3.69 R
5026 5564 1.064758 TCTGCCAAACACCAGTGAAGT 60.065 47.619 4.48 0.00 0.00 3.01 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
23 24 6.417191 TGATTTAGTGCTACATTTTCCGTC 57.583 37.500 0.00 0.00 0.00 4.79
24 25 5.353123 TGATTTAGTGCTACATTTTCCGTCC 59.647 40.000 0.00 0.00 0.00 4.79
25 26 2.851263 AGTGCTACATTTTCCGTCCA 57.149 45.000 0.00 0.00 0.00 4.02
26 27 2.423577 AGTGCTACATTTTCCGTCCAC 58.576 47.619 0.00 0.00 0.00 4.02
27 28 2.038557 AGTGCTACATTTTCCGTCCACT 59.961 45.455 0.00 0.00 0.00 4.00
28 29 3.259876 AGTGCTACATTTTCCGTCCACTA 59.740 43.478 0.00 0.00 31.32 2.74
29 30 3.998341 GTGCTACATTTTCCGTCCACTAA 59.002 43.478 0.00 0.00 0.00 2.24
30 31 4.092968 GTGCTACATTTTCCGTCCACTAAG 59.907 45.833 0.00 0.00 0.00 2.18
31 32 3.621715 GCTACATTTTCCGTCCACTAAGG 59.378 47.826 0.00 0.00 39.47 2.69
32 33 2.433436 ACATTTTCCGTCCACTAAGGC 58.567 47.619 0.00 0.00 37.29 4.35
33 34 1.743394 CATTTTCCGTCCACTAAGGCC 59.257 52.381 0.00 0.00 37.29 5.19
34 35 0.037160 TTTTCCGTCCACTAAGGCCC 59.963 55.000 0.00 0.00 37.29 5.80
35 36 0.838987 TTTCCGTCCACTAAGGCCCT 60.839 55.000 0.00 0.00 37.29 5.19
36 37 1.550130 TTCCGTCCACTAAGGCCCTG 61.550 60.000 0.00 0.00 37.29 4.45
37 38 2.291043 CCGTCCACTAAGGCCCTGT 61.291 63.158 0.00 0.00 37.29 4.00
38 39 1.677552 CGTCCACTAAGGCCCTGTT 59.322 57.895 0.00 0.00 37.29 3.16
39 40 0.673644 CGTCCACTAAGGCCCTGTTG 60.674 60.000 0.00 0.00 37.29 3.33
40 41 0.322546 GTCCACTAAGGCCCTGTTGG 60.323 60.000 0.00 1.19 37.29 3.77
61 62 3.963428 GAGTCACTCCAGCTCCTAAAA 57.037 47.619 0.00 0.00 0.00 1.52
62 63 4.273148 GAGTCACTCCAGCTCCTAAAAA 57.727 45.455 0.00 0.00 0.00 1.94
63 64 4.837972 GAGTCACTCCAGCTCCTAAAAAT 58.162 43.478 0.00 0.00 0.00 1.82
64 65 5.978814 GAGTCACTCCAGCTCCTAAAAATA 58.021 41.667 0.00 0.00 0.00 1.40
65 66 5.735766 AGTCACTCCAGCTCCTAAAAATAC 58.264 41.667 0.00 0.00 0.00 1.89
66 67 4.567159 GTCACTCCAGCTCCTAAAAATACG 59.433 45.833 0.00 0.00 0.00 3.06
67 68 4.464951 TCACTCCAGCTCCTAAAAATACGA 59.535 41.667 0.00 0.00 0.00 3.43
68 69 4.806247 CACTCCAGCTCCTAAAAATACGAG 59.194 45.833 0.00 0.00 0.00 4.18
69 70 4.141914 ACTCCAGCTCCTAAAAATACGAGG 60.142 45.833 0.00 0.00 0.00 4.63
70 71 4.028131 TCCAGCTCCTAAAAATACGAGGA 58.972 43.478 0.00 0.00 37.02 3.71
75 76 3.793559 TCCTAAAAATACGAGGAGCTGC 58.206 45.455 0.00 0.00 34.36 5.25
76 77 2.540101 CCTAAAAATACGAGGAGCTGCG 59.460 50.000 0.00 0.00 31.45 5.18
77 78 1.369625 AAAAATACGAGGAGCTGCGG 58.630 50.000 0.00 0.00 0.00 5.69
78 79 0.535335 AAAATACGAGGAGCTGCGGA 59.465 50.000 0.00 0.00 0.00 5.54
79 80 0.103208 AAATACGAGGAGCTGCGGAG 59.897 55.000 0.00 0.00 0.00 4.63
80 81 1.038130 AATACGAGGAGCTGCGGAGT 61.038 55.000 5.62 4.07 0.00 3.85
81 82 0.179026 ATACGAGGAGCTGCGGAGTA 60.179 55.000 5.62 11.31 0.00 2.59
82 83 0.179026 TACGAGGAGCTGCGGAGTAT 60.179 55.000 5.62 0.00 0.00 2.12
83 84 1.284408 CGAGGAGCTGCGGAGTATC 59.716 63.158 5.62 4.25 0.00 2.24
84 85 1.169661 CGAGGAGCTGCGGAGTATCT 61.170 60.000 5.62 0.09 33.73 1.98
85 86 0.313672 GAGGAGCTGCGGAGTATCTG 59.686 60.000 5.62 0.00 46.81 2.90
86 87 0.396417 AGGAGCTGCGGAGTATCTGT 60.396 55.000 5.62 0.00 45.47 3.41
87 88 0.461961 GGAGCTGCGGAGTATCTGTT 59.538 55.000 5.62 0.00 45.47 3.16
88 89 1.134670 GGAGCTGCGGAGTATCTGTTT 60.135 52.381 5.62 0.00 45.47 2.83
89 90 2.197577 GAGCTGCGGAGTATCTGTTTC 58.802 52.381 5.62 0.00 45.47 2.78
90 91 1.134670 AGCTGCGGAGTATCTGTTTCC 60.135 52.381 5.62 0.00 45.47 3.13
91 92 1.941325 CTGCGGAGTATCTGTTTCCC 58.059 55.000 0.00 0.00 45.47 3.97
92 93 1.207089 CTGCGGAGTATCTGTTTCCCA 59.793 52.381 0.00 0.00 45.47 4.37
93 94 1.207089 TGCGGAGTATCTGTTTCCCAG 59.793 52.381 0.00 0.00 45.47 4.45
94 95 1.941325 CGGAGTATCTGTTTCCCAGC 58.059 55.000 0.00 0.00 41.25 4.85
95 96 1.482593 CGGAGTATCTGTTTCCCAGCT 59.517 52.381 0.00 0.00 41.25 4.24
96 97 2.093447 CGGAGTATCTGTTTCCCAGCTT 60.093 50.000 0.00 0.00 41.25 3.74
97 98 3.536570 GGAGTATCTGTTTCCCAGCTTC 58.463 50.000 0.00 0.00 41.25 3.86
98 99 3.190874 GAGTATCTGTTTCCCAGCTTCG 58.809 50.000 0.00 0.00 41.25 3.79
99 100 2.567615 AGTATCTGTTTCCCAGCTTCGT 59.432 45.455 0.00 0.00 41.25 3.85
100 101 1.813513 ATCTGTTTCCCAGCTTCGTG 58.186 50.000 0.00 0.00 41.25 4.35
101 102 0.884704 TCTGTTTCCCAGCTTCGTGC 60.885 55.000 0.00 0.00 41.25 5.34
102 103 1.856265 CTGTTTCCCAGCTTCGTGCC 61.856 60.000 0.00 0.00 44.23 5.01
103 104 1.600916 GTTTCCCAGCTTCGTGCCT 60.601 57.895 0.00 0.00 44.23 4.75
104 105 1.150536 TTTCCCAGCTTCGTGCCTT 59.849 52.632 0.00 0.00 44.23 4.35
105 106 0.467290 TTTCCCAGCTTCGTGCCTTT 60.467 50.000 0.00 0.00 44.23 3.11
106 107 0.467290 TTCCCAGCTTCGTGCCTTTT 60.467 50.000 0.00 0.00 44.23 2.27
107 108 0.398696 TCCCAGCTTCGTGCCTTTTA 59.601 50.000 0.00 0.00 44.23 1.52
108 109 1.202830 TCCCAGCTTCGTGCCTTTTAA 60.203 47.619 0.00 0.00 44.23 1.52
109 110 1.068541 CCCAGCTTCGTGCCTTTTAAC 60.069 52.381 0.00 0.00 44.23 2.01
110 111 1.880027 CCAGCTTCGTGCCTTTTAACT 59.120 47.619 0.00 0.00 44.23 2.24
111 112 2.095718 CCAGCTTCGTGCCTTTTAACTC 60.096 50.000 0.00 0.00 44.23 3.01
112 113 2.808543 CAGCTTCGTGCCTTTTAACTCT 59.191 45.455 0.00 0.00 44.23 3.24
113 114 3.994392 CAGCTTCGTGCCTTTTAACTCTA 59.006 43.478 0.00 0.00 44.23 2.43
114 115 4.092091 CAGCTTCGTGCCTTTTAACTCTAG 59.908 45.833 0.00 0.00 44.23 2.43
115 116 3.181519 GCTTCGTGCCTTTTAACTCTAGC 60.182 47.826 0.00 0.00 35.15 3.42
116 117 3.955650 TCGTGCCTTTTAACTCTAGCT 57.044 42.857 0.00 0.00 0.00 3.32
117 118 3.846360 TCGTGCCTTTTAACTCTAGCTC 58.154 45.455 0.00 0.00 0.00 4.09
118 119 2.930682 CGTGCCTTTTAACTCTAGCTCC 59.069 50.000 0.00 0.00 0.00 4.70
119 120 2.930682 GTGCCTTTTAACTCTAGCTCCG 59.069 50.000 0.00 0.00 0.00 4.63
120 121 2.093658 TGCCTTTTAACTCTAGCTCCGG 60.094 50.000 0.00 0.00 0.00 5.14
121 122 2.742204 GCCTTTTAACTCTAGCTCCGGG 60.742 54.545 0.00 0.00 0.00 5.73
122 123 2.500504 CCTTTTAACTCTAGCTCCGGGT 59.499 50.000 0.00 0.00 0.00 5.28
123 124 3.522553 CTTTTAACTCTAGCTCCGGGTG 58.477 50.000 0.00 0.00 0.00 4.61
124 125 2.519771 TTAACTCTAGCTCCGGGTGA 57.480 50.000 0.00 0.00 0.00 4.02
125 126 2.054232 TAACTCTAGCTCCGGGTGAG 57.946 55.000 0.00 5.14 44.47 3.51
126 127 0.684805 AACTCTAGCTCCGGGTGAGG 60.685 60.000 0.00 0.00 41.73 3.86
127 128 1.227664 CTCTAGCTCCGGGTGAGGA 59.772 63.158 0.00 0.00 41.73 3.71
133 134 2.603473 TCCGGGTGAGGAGTGGTG 60.603 66.667 0.00 0.00 34.92 4.17
134 135 3.706373 CCGGGTGAGGAGTGGTGG 61.706 72.222 0.00 0.00 0.00 4.61
135 136 4.394712 CGGGTGAGGAGTGGTGGC 62.395 72.222 0.00 0.00 0.00 5.01
136 137 4.394712 GGGTGAGGAGTGGTGGCG 62.395 72.222 0.00 0.00 0.00 5.69
137 138 3.626924 GGTGAGGAGTGGTGGCGT 61.627 66.667 0.00 0.00 0.00 5.68
138 139 2.357517 GTGAGGAGTGGTGGCGTG 60.358 66.667 0.00 0.00 0.00 5.34
139 140 3.625897 TGAGGAGTGGTGGCGTGG 61.626 66.667 0.00 0.00 0.00 4.94
140 141 3.626924 GAGGAGTGGTGGCGTGGT 61.627 66.667 0.00 0.00 0.00 4.16
141 142 3.883744 GAGGAGTGGTGGCGTGGTG 62.884 68.421 0.00 0.00 0.00 4.17
147 148 4.699522 GGTGGCGTGGTGGGACTC 62.700 72.222 0.00 0.00 0.00 3.36
148 149 4.699522 GTGGCGTGGTGGGACTCC 62.700 72.222 0.00 0.00 43.26 3.85
151 152 3.998672 GCGTGGTGGGACTCCGAA 61.999 66.667 0.00 0.00 46.43 4.30
152 153 2.048503 CGTGGTGGGACTCCGAAC 60.049 66.667 0.00 0.00 46.43 3.95
153 154 2.863346 CGTGGTGGGACTCCGAACA 61.863 63.158 0.00 0.00 46.43 3.18
154 155 1.004918 GTGGTGGGACTCCGAACAG 60.005 63.158 0.00 0.00 46.43 3.16
155 156 2.214216 TGGTGGGACTCCGAACAGG 61.214 63.158 0.00 0.00 46.43 4.00
156 157 2.663196 GTGGGACTCCGAACAGGG 59.337 66.667 0.00 0.00 41.52 4.45
157 158 2.203182 TGGGACTCCGAACAGGGT 59.797 61.111 0.00 0.00 41.52 4.34
158 159 1.911766 TGGGACTCCGAACAGGGTC 60.912 63.158 0.00 0.00 41.52 4.46
159 160 1.609794 GGGACTCCGAACAGGGTCT 60.610 63.158 0.00 0.00 41.52 3.85
160 161 0.324091 GGGACTCCGAACAGGGTCTA 60.324 60.000 0.00 0.00 41.52 2.59
161 162 1.553706 GGACTCCGAACAGGGTCTAA 58.446 55.000 0.00 0.00 41.52 2.10
162 163 1.477295 GGACTCCGAACAGGGTCTAAG 59.523 57.143 0.00 0.00 41.52 2.18
163 164 2.169330 GACTCCGAACAGGGTCTAAGT 58.831 52.381 0.00 0.00 41.52 2.24
164 165 2.561858 GACTCCGAACAGGGTCTAAGTT 59.438 50.000 0.00 0.00 41.52 2.66
165 166 2.970640 ACTCCGAACAGGGTCTAAGTTT 59.029 45.455 0.00 0.00 41.52 2.66
166 167 3.244112 ACTCCGAACAGGGTCTAAGTTTG 60.244 47.826 0.00 0.00 41.52 2.93
167 168 1.804748 CCGAACAGGGTCTAAGTTTGC 59.195 52.381 0.00 0.00 35.97 3.68
168 169 1.804748 CGAACAGGGTCTAAGTTTGCC 59.195 52.381 0.00 0.00 0.00 4.52
169 170 1.804748 GAACAGGGTCTAAGTTTGCCG 59.195 52.381 0.00 0.00 0.00 5.69
170 171 0.036306 ACAGGGTCTAAGTTTGCCGG 59.964 55.000 0.00 0.00 0.00 6.13
171 172 0.323629 CAGGGTCTAAGTTTGCCGGA 59.676 55.000 5.05 0.00 0.00 5.14
172 173 1.061546 AGGGTCTAAGTTTGCCGGAA 58.938 50.000 5.05 0.00 0.00 4.30
173 174 1.003233 AGGGTCTAAGTTTGCCGGAAG 59.997 52.381 5.05 0.00 0.00 3.46
174 175 1.002773 GGGTCTAAGTTTGCCGGAAGA 59.997 52.381 5.05 0.00 0.00 2.87
175 176 2.551504 GGGTCTAAGTTTGCCGGAAGAA 60.552 50.000 5.05 0.00 0.00 2.52
176 177 3.143728 GGTCTAAGTTTGCCGGAAGAAA 58.856 45.455 5.05 0.00 0.00 2.52
177 178 3.566742 GGTCTAAGTTTGCCGGAAGAAAA 59.433 43.478 5.05 0.00 0.00 2.29
178 179 4.534168 GTCTAAGTTTGCCGGAAGAAAAC 58.466 43.478 5.05 9.94 37.58 2.43
179 180 4.275196 GTCTAAGTTTGCCGGAAGAAAACT 59.725 41.667 5.05 12.18 44.30 2.66
180 181 3.710326 AAGTTTGCCGGAAGAAAACTC 57.290 42.857 19.02 0.00 42.79 3.01
181 182 2.932261 AGTTTGCCGGAAGAAAACTCT 58.068 42.857 5.05 0.00 41.06 3.24
182 183 3.288092 AGTTTGCCGGAAGAAAACTCTT 58.712 40.909 5.05 0.00 41.06 2.85
183 184 3.699538 AGTTTGCCGGAAGAAAACTCTTT 59.300 39.130 5.05 0.00 41.06 2.52
184 185 4.159693 AGTTTGCCGGAAGAAAACTCTTTT 59.840 37.500 5.05 0.00 41.06 2.27
185 186 4.729227 TTGCCGGAAGAAAACTCTTTTT 57.271 36.364 5.05 0.00 37.65 1.94
193 194 3.430333 GAAAACTCTTTTTCGTGGGCA 57.570 42.857 0.00 0.00 40.90 5.36
194 195 3.977427 GAAAACTCTTTTTCGTGGGCAT 58.023 40.909 0.00 0.00 40.90 4.40
195 196 4.368315 GAAAACTCTTTTTCGTGGGCATT 58.632 39.130 0.00 0.00 40.90 3.56
196 197 4.400529 AAACTCTTTTTCGTGGGCATTT 57.599 36.364 0.00 0.00 0.00 2.32
197 198 4.400529 AACTCTTTTTCGTGGGCATTTT 57.599 36.364 0.00 0.00 0.00 1.82
198 199 3.977427 ACTCTTTTTCGTGGGCATTTTC 58.023 40.909 0.00 0.00 0.00 2.29
199 200 3.636764 ACTCTTTTTCGTGGGCATTTTCT 59.363 39.130 0.00 0.00 0.00 2.52
200 201 3.976169 TCTTTTTCGTGGGCATTTTCTG 58.024 40.909 0.00 0.00 0.00 3.02
201 202 2.810439 TTTTCGTGGGCATTTTCTGG 57.190 45.000 0.00 0.00 0.00 3.86
202 203 0.965439 TTTCGTGGGCATTTTCTGGG 59.035 50.000 0.00 0.00 0.00 4.45
203 204 0.111446 TTCGTGGGCATTTTCTGGGA 59.889 50.000 0.00 0.00 0.00 4.37
218 219 2.489938 TGGGAACAGTATGGTTGCTC 57.510 50.000 0.00 0.00 33.00 4.26
237 238 9.289782 GGTTGCTCATATCCAAATTTAGAGTAT 57.710 33.333 0.00 0.00 0.00 2.12
421 431 5.753438 CGCTCAAAAGCCACTATTATCAGTA 59.247 40.000 0.00 0.00 46.34 2.74
425 435 8.079211 TCAAAAGCCACTATTATCAGTAGTCT 57.921 34.615 0.00 0.00 30.24 3.24
435 445 6.782082 ATTATCAGTAGTCTGCTTCACTCA 57.218 37.500 0.00 0.00 41.10 3.41
437 447 3.491342 TCAGTAGTCTGCTTCACTCACT 58.509 45.455 0.00 0.00 41.10 3.41
440 450 2.810439 AGTCTGCTTCACTCACTCAC 57.190 50.000 0.00 0.00 0.00 3.51
473 483 1.000060 CCCTCAACCAACAGCAACATG 60.000 52.381 0.00 0.00 0.00 3.21
482 500 3.181517 CCAACAGCAACATGAGTACATCG 60.182 47.826 0.00 0.00 34.15 3.84
535 566 3.643595 TACACCCCAGCTGCATGCC 62.644 63.158 16.68 0.00 44.23 4.40
569 600 5.447548 CGTACACTTGAGAGTTAGAGTAGGC 60.448 48.000 0.00 0.00 32.54 3.93
570 601 3.764972 ACACTTGAGAGTTAGAGTAGGCC 59.235 47.826 0.00 0.00 32.54 5.19
675 893 3.866582 CCCTCCCTCCGATGCACC 61.867 72.222 0.00 0.00 0.00 5.01
712 934 5.844004 TCTCTCTCTACACTTTCAAACCAC 58.156 41.667 0.00 0.00 0.00 4.16
771 995 2.250031 TGTTGAGAAGCCCAATGCATT 58.750 42.857 5.99 5.99 44.83 3.56
800 1024 6.605119 CAAGAACCCTACCCTATTCATTCAT 58.395 40.000 0.00 0.00 0.00 2.57
828 1052 2.427095 AGGACACAAGCAAACACCTTTC 59.573 45.455 0.00 0.00 0.00 2.62
847 1071 5.700373 CCTTTCAGAGTTTTGAGGAAGAGAG 59.300 44.000 0.00 0.00 0.00 3.20
850 1074 4.526262 TCAGAGTTTTGAGGAAGAGAGAGG 59.474 45.833 0.00 0.00 0.00 3.69
852 1076 3.580895 GAGTTTTGAGGAAGAGAGAGGGT 59.419 47.826 0.00 0.00 0.00 4.34
854 1078 2.704190 TTGAGGAAGAGAGAGGGTGT 57.296 50.000 0.00 0.00 0.00 4.16
855 1079 1.930251 TGAGGAAGAGAGAGGGTGTG 58.070 55.000 0.00 0.00 0.00 3.82
856 1080 1.148027 TGAGGAAGAGAGAGGGTGTGT 59.852 52.381 0.00 0.00 0.00 3.72
857 1081 1.548269 GAGGAAGAGAGAGGGTGTGTG 59.452 57.143 0.00 0.00 0.00 3.82
858 1082 1.133009 AGGAAGAGAGAGGGTGTGTGT 60.133 52.381 0.00 0.00 0.00 3.72
882 1106 5.905331 TGAGAGAGAATCCTAGAGAGAGAGT 59.095 44.000 0.00 0.00 33.66 3.24
894 1118 2.939103 GAGAGAGAGTGAGAGTGAGAGC 59.061 54.545 0.00 0.00 0.00 4.09
895 1119 2.573462 AGAGAGAGTGAGAGTGAGAGCT 59.427 50.000 0.00 0.00 0.00 4.09
902 1156 0.457035 GAGAGTGAGAGCTGCCTCAG 59.543 60.000 17.37 0.00 43.15 3.35
913 1167 1.651240 CTGCCTCAGTTCCATTGCCG 61.651 60.000 0.00 0.00 0.00 5.69
1099 1358 4.044825 TCTTACTCAACCTCCTCCTCTTCT 59.955 45.833 0.00 0.00 0.00 2.85
1117 1376 3.706373 CCTCCACCTCCACCACCG 61.706 72.222 0.00 0.00 0.00 4.94
1167 1441 0.758123 CCTTCCTCTCCTCATGGCTC 59.242 60.000 0.00 0.00 0.00 4.70
1269 1543 2.909965 GGCAGGGCGGTTGTTTCA 60.910 61.111 0.00 0.00 0.00 2.69
1272 1546 1.654220 CAGGGCGGTTGTTTCAGTG 59.346 57.895 0.00 0.00 0.00 3.66
1275 1549 0.818040 GGGCGGTTGTTTCAGTGACT 60.818 55.000 0.00 0.00 0.00 3.41
1671 1945 3.917760 CACGATCTCTCCGGCCCC 61.918 72.222 0.00 0.00 0.00 5.80
1686 1960 2.666098 CCCCATCCCCGACTCGTTT 61.666 63.158 0.00 0.00 0.00 3.60
1986 2260 2.032681 AGCTTCGGCAACCTCACC 59.967 61.111 0.00 0.00 44.74 4.02
2092 2366 2.874086 CTGATGCTCAGTGACAACAACA 59.126 45.455 0.00 0.00 39.58 3.33
2109 2383 3.014538 ATCACCGGCACCATCCCA 61.015 61.111 0.00 0.00 0.00 4.37
2472 2746 1.983119 GCATCACCGGGGAGATTCCA 61.983 60.000 14.24 0.00 38.64 3.53
2616 2898 2.752358 CTCACTGGAGCCTTGCCA 59.248 61.111 0.00 0.00 33.67 4.92
2673 2955 0.178068 ACGTCTCACACAACCAGCTT 59.822 50.000 0.00 0.00 0.00 3.74
3060 3342 2.050350 CCTCCCGGACACGAAGCTA 61.050 63.158 0.73 0.00 44.60 3.32
3138 3420 2.235016 CGACGTGTGCTTCGTTGGT 61.235 57.895 0.00 0.00 41.64 3.67
3299 3584 4.966787 GGTGGGCGTCAAGGGCAA 62.967 66.667 0.00 0.00 0.00 4.52
3300 3585 2.676471 GTGGGCGTCAAGGGCAAT 60.676 61.111 0.00 0.00 0.00 3.56
3306 3591 1.603455 CGTCAAGGGCAATGGTGGT 60.603 57.895 0.00 0.00 0.00 4.16
3390 3675 1.270907 TCCAGAAGGTGAGCTTCTCC 58.729 55.000 22.70 0.00 38.93 3.71
3396 3681 1.216710 GGTGAGCTTCTCCGTGGAG 59.783 63.158 9.73 9.73 43.21 3.86
3612 3897 1.793613 GCACAAGAACATCGTGCGC 60.794 57.895 0.00 0.00 45.69 6.09
3988 4294 4.046286 ACCAACCTCCATTTCTGCATAA 57.954 40.909 0.00 0.00 0.00 1.90
4018 4508 5.530171 GTCCGATATGACTCTACTGTTACCA 59.470 44.000 0.00 0.00 32.39 3.25
4066 4576 3.095102 TGGTGTTTGATTGTGTGCATG 57.905 42.857 0.00 0.00 0.00 4.06
4070 4580 5.221402 TGGTGTTTGATTGTGTGCATGTTAT 60.221 36.000 0.00 0.00 0.00 1.89
4071 4581 6.015940 TGGTGTTTGATTGTGTGCATGTTATA 60.016 34.615 0.00 0.00 0.00 0.98
4120 4630 8.128582 TCATGATTTGTTTCCGATTAATGCTAC 58.871 33.333 0.00 0.00 0.00 3.58
4232 4743 1.802880 GCAGAGTACGGGTACATGCTG 60.803 57.143 21.81 18.78 42.57 4.41
4292 4803 2.359230 GTGCTGGAGGTGCTGACC 60.359 66.667 0.00 0.00 43.52 4.02
4409 4920 3.770040 CAGGGGCGATCCGACACA 61.770 66.667 0.00 0.00 43.01 3.72
4425 4936 1.566211 CACAGAGGTGGAGGAGATGT 58.434 55.000 0.00 0.00 41.45 3.06
4442 4953 2.672651 TTGCAGGTCATGGGCGTG 60.673 61.111 0.00 0.00 0.00 5.34
4652 5166 2.048597 GCCACCACATCGACGTCA 60.049 61.111 17.16 3.13 0.00 4.35
4897 5435 5.159273 ACTTTGAGGATGAAGAAGAGGAC 57.841 43.478 0.00 0.00 0.00 3.85
4905 5443 6.883744 AGGATGAAGAAGAGGACATTAGAAC 58.116 40.000 0.00 0.00 0.00 3.01
4922 5460 8.410912 ACATTAGAACGAAAACTAAGGCTTTTT 58.589 29.630 4.45 0.00 34.95 1.94
5011 5549 3.181367 GCCATGTCACGAAGGCAG 58.819 61.111 0.00 0.00 46.26 4.85
5013 5551 1.003355 CCATGTCACGAAGGCAGGT 60.003 57.895 0.00 0.00 0.00 4.00
5014 5552 1.300971 CCATGTCACGAAGGCAGGTG 61.301 60.000 0.00 0.00 35.50 4.00
5015 5553 0.603707 CATGTCACGAAGGCAGGTGT 60.604 55.000 0.00 0.00 35.67 4.16
5022 5560 1.507141 CGAAGGCAGGTGTTGTCCAC 61.507 60.000 0.00 0.00 43.74 4.02
5026 5564 0.533308 GGCAGGTGTTGTCCACGTTA 60.533 55.000 0.00 0.00 45.52 3.18
5276 5879 7.442364 GCTAGTAAGTGATTTGATGATGCCTTA 59.558 37.037 0.00 0.00 0.00 2.69
5302 5905 6.649141 TGTGTTGAGCTAGTAGTGTTTAATGG 59.351 38.462 0.00 0.00 0.00 3.16
5350 5953 2.225467 TGCCGTGTCATGTCAAATTCA 58.775 42.857 0.00 0.00 0.00 2.57
5360 5963 8.345565 GTGTCATGTCAAATTCACTAAGTTTCT 58.654 33.333 0.00 0.00 0.00 2.52
5392 5995 0.538287 GGAGACAACAAAGGGCTGCT 60.538 55.000 0.00 0.00 0.00 4.24
5541 6144 8.964476 ATACTCATCAACTTGAAATAACCGAT 57.036 30.769 0.00 0.00 0.00 4.18
5606 6209 7.080724 GTCTTTGCACTCTATTTGGAAGAAAG 58.919 38.462 0.00 0.00 0.00 2.62
5666 6269 4.669206 TTTTCATGTGTGGAATGCTGTT 57.331 36.364 0.00 0.00 0.00 3.16
5691 6294 5.362143 TGATTCAAGTTCATGTGGTTCCAAA 59.638 36.000 0.00 0.00 0.00 3.28
5750 6353 7.719633 ACTTACAAGTGGAGAAAAGCTATTCAA 59.280 33.333 0.00 0.00 37.98 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.353123 TGGACGGAAAATGTAGCACTAAATC 59.647 40.000 0.00 0.00 0.00 2.17
4 5 3.998341 GTGGACGGAAAATGTAGCACTAA 59.002 43.478 0.00 0.00 0.00 2.24
5 6 3.259876 AGTGGACGGAAAATGTAGCACTA 59.740 43.478 0.00 0.00 0.00 2.74
6 7 2.038557 AGTGGACGGAAAATGTAGCACT 59.961 45.455 0.00 0.00 0.00 4.40
8 9 2.851263 AGTGGACGGAAAATGTAGCA 57.149 45.000 0.00 0.00 0.00 3.49
9 10 3.621715 CCTTAGTGGACGGAAAATGTAGC 59.378 47.826 0.00 0.00 38.35 3.58
10 11 3.621715 GCCTTAGTGGACGGAAAATGTAG 59.378 47.826 0.00 0.00 38.35 2.74
11 12 3.602483 GCCTTAGTGGACGGAAAATGTA 58.398 45.455 0.00 0.00 38.35 2.29
12 13 2.433436 GCCTTAGTGGACGGAAAATGT 58.567 47.619 0.00 0.00 38.35 2.71
13 14 1.743394 GGCCTTAGTGGACGGAAAATG 59.257 52.381 0.00 0.00 38.35 2.32
14 15 2.124277 GGCCTTAGTGGACGGAAAAT 57.876 50.000 0.00 0.00 38.35 1.82
15 16 3.637184 GGCCTTAGTGGACGGAAAA 57.363 52.632 0.00 0.00 38.35 2.29
21 22 0.322546 CCAACAGGGCCTTAGTGGAC 60.323 60.000 18.19 0.00 45.48 4.02
22 23 1.497309 CCCAACAGGGCCTTAGTGGA 61.497 60.000 22.75 0.00 35.34 4.02
23 24 1.000896 CCCAACAGGGCCTTAGTGG 60.001 63.158 16.69 16.69 35.34 4.00
24 25 0.035056 CTCCCAACAGGGCCTTAGTG 60.035 60.000 1.32 1.52 42.73 2.74
25 26 0.475828 ACTCCCAACAGGGCCTTAGT 60.476 55.000 1.32 0.00 42.73 2.24
26 27 0.253327 GACTCCCAACAGGGCCTTAG 59.747 60.000 1.32 0.00 42.73 2.18
27 28 0.474854 TGACTCCCAACAGGGCCTTA 60.475 55.000 1.32 0.00 42.73 2.69
28 29 1.774217 TGACTCCCAACAGGGCCTT 60.774 57.895 1.32 0.00 42.73 4.35
29 30 2.121963 TGACTCCCAACAGGGCCT 60.122 61.111 0.00 0.00 42.73 5.19
30 31 2.034221 GTGACTCCCAACAGGGCC 59.966 66.667 0.00 0.00 42.73 5.80
31 32 1.003233 GAGTGACTCCCAACAGGGC 60.003 63.158 0.00 0.00 42.73 5.19
32 33 1.679898 GGAGTGACTCCCAACAGGG 59.320 63.158 20.95 0.00 44.36 4.45
41 42 3.963428 TTTTAGGAGCTGGAGTGACTC 57.037 47.619 3.47 3.47 0.00 3.36
42 43 4.917906 ATTTTTAGGAGCTGGAGTGACT 57.082 40.909 0.00 0.00 0.00 3.41
43 44 4.567159 CGTATTTTTAGGAGCTGGAGTGAC 59.433 45.833 0.00 0.00 0.00 3.67
44 45 4.464951 TCGTATTTTTAGGAGCTGGAGTGA 59.535 41.667 0.00 0.00 0.00 3.41
45 46 4.755411 TCGTATTTTTAGGAGCTGGAGTG 58.245 43.478 0.00 0.00 0.00 3.51
46 47 4.141914 CCTCGTATTTTTAGGAGCTGGAGT 60.142 45.833 0.00 0.00 32.37 3.85
47 48 4.099573 TCCTCGTATTTTTAGGAGCTGGAG 59.900 45.833 0.00 0.00 34.46 3.86
48 49 4.028131 TCCTCGTATTTTTAGGAGCTGGA 58.972 43.478 0.00 0.00 34.46 3.86
49 50 4.402056 TCCTCGTATTTTTAGGAGCTGG 57.598 45.455 0.00 0.00 34.46 4.85
54 55 3.737047 CGCAGCTCCTCGTATTTTTAGGA 60.737 47.826 0.00 0.00 37.07 2.94
55 56 2.540101 CGCAGCTCCTCGTATTTTTAGG 59.460 50.000 0.00 0.00 0.00 2.69
56 57 2.540101 CCGCAGCTCCTCGTATTTTTAG 59.460 50.000 0.00 0.00 0.00 1.85
57 58 2.166870 TCCGCAGCTCCTCGTATTTTTA 59.833 45.455 0.00 0.00 0.00 1.52
58 59 1.066430 TCCGCAGCTCCTCGTATTTTT 60.066 47.619 0.00 0.00 0.00 1.94
59 60 0.535335 TCCGCAGCTCCTCGTATTTT 59.465 50.000 0.00 0.00 0.00 1.82
60 61 0.103208 CTCCGCAGCTCCTCGTATTT 59.897 55.000 0.00 0.00 0.00 1.40
61 62 1.038130 ACTCCGCAGCTCCTCGTATT 61.038 55.000 0.00 0.00 0.00 1.89
62 63 0.179026 TACTCCGCAGCTCCTCGTAT 60.179 55.000 0.00 0.00 0.00 3.06
63 64 0.179026 ATACTCCGCAGCTCCTCGTA 60.179 55.000 0.00 0.00 0.00 3.43
64 65 1.448922 GATACTCCGCAGCTCCTCGT 61.449 60.000 0.00 0.00 0.00 4.18
65 66 1.169661 AGATACTCCGCAGCTCCTCG 61.170 60.000 0.00 0.00 0.00 4.63
66 67 0.313672 CAGATACTCCGCAGCTCCTC 59.686 60.000 0.00 0.00 0.00 3.71
67 68 0.396417 ACAGATACTCCGCAGCTCCT 60.396 55.000 0.00 0.00 0.00 3.69
68 69 0.461961 AACAGATACTCCGCAGCTCC 59.538 55.000 0.00 0.00 0.00 4.70
69 70 2.197577 GAAACAGATACTCCGCAGCTC 58.802 52.381 0.00 0.00 0.00 4.09
70 71 1.134670 GGAAACAGATACTCCGCAGCT 60.135 52.381 0.00 0.00 0.00 4.24
71 72 1.291132 GGAAACAGATACTCCGCAGC 58.709 55.000 0.00 0.00 0.00 5.25
72 73 1.207089 TGGGAAACAGATACTCCGCAG 59.793 52.381 0.00 0.00 0.00 5.18
73 74 1.271856 TGGGAAACAGATACTCCGCA 58.728 50.000 0.00 0.00 0.00 5.69
84 85 1.896660 GGCACGAAGCTGGGAAACA 60.897 57.895 0.00 0.00 44.79 2.83
85 86 1.172812 AAGGCACGAAGCTGGGAAAC 61.173 55.000 0.00 0.00 44.79 2.78
86 87 0.467290 AAAGGCACGAAGCTGGGAAA 60.467 50.000 0.00 0.00 44.79 3.13
87 88 0.467290 AAAAGGCACGAAGCTGGGAA 60.467 50.000 0.00 0.00 44.79 3.97
88 89 0.398696 TAAAAGGCACGAAGCTGGGA 59.601 50.000 0.00 0.00 44.79 4.37
89 90 1.068541 GTTAAAAGGCACGAAGCTGGG 60.069 52.381 0.00 0.00 44.79 4.45
90 91 1.880027 AGTTAAAAGGCACGAAGCTGG 59.120 47.619 0.00 0.00 44.79 4.85
91 92 2.808543 AGAGTTAAAAGGCACGAAGCTG 59.191 45.455 0.00 0.00 44.79 4.24
92 93 3.127425 AGAGTTAAAAGGCACGAAGCT 57.873 42.857 0.00 0.00 44.79 3.74
93 94 3.181519 GCTAGAGTTAAAAGGCACGAAGC 60.182 47.826 0.00 0.00 44.65 3.86
94 95 4.246458 AGCTAGAGTTAAAAGGCACGAAG 58.754 43.478 0.00 0.00 0.00 3.79
95 96 4.243270 GAGCTAGAGTTAAAAGGCACGAA 58.757 43.478 0.00 0.00 0.00 3.85
96 97 3.368116 GGAGCTAGAGTTAAAAGGCACGA 60.368 47.826 0.00 0.00 0.00 4.35
97 98 2.930682 GGAGCTAGAGTTAAAAGGCACG 59.069 50.000 0.00 0.00 0.00 5.34
98 99 2.930682 CGGAGCTAGAGTTAAAAGGCAC 59.069 50.000 0.00 0.00 0.00 5.01
99 100 2.093658 CCGGAGCTAGAGTTAAAAGGCA 60.094 50.000 0.00 0.00 0.00 4.75
100 101 2.552031 CCGGAGCTAGAGTTAAAAGGC 58.448 52.381 0.00 0.00 0.00 4.35
101 102 2.500504 ACCCGGAGCTAGAGTTAAAAGG 59.499 50.000 0.73 0.00 0.00 3.11
102 103 3.194968 TCACCCGGAGCTAGAGTTAAAAG 59.805 47.826 0.73 0.00 0.00 2.27
103 104 3.167485 TCACCCGGAGCTAGAGTTAAAA 58.833 45.455 0.73 0.00 0.00 1.52
104 105 2.758979 CTCACCCGGAGCTAGAGTTAAA 59.241 50.000 0.73 0.00 36.69 1.52
105 106 2.376109 CTCACCCGGAGCTAGAGTTAA 58.624 52.381 0.73 0.00 36.69 2.01
106 107 1.409802 CCTCACCCGGAGCTAGAGTTA 60.410 57.143 0.73 0.00 42.62 2.24
107 108 0.684805 CCTCACCCGGAGCTAGAGTT 60.685 60.000 0.73 0.00 42.62 3.01
108 109 1.076632 CCTCACCCGGAGCTAGAGT 60.077 63.158 0.73 0.00 42.62 3.24
109 110 0.821711 CTCCTCACCCGGAGCTAGAG 60.822 65.000 0.73 2.15 43.69 2.43
110 111 1.227664 CTCCTCACCCGGAGCTAGA 59.772 63.158 0.73 0.00 43.69 2.43
111 112 3.849064 CTCCTCACCCGGAGCTAG 58.151 66.667 0.73 0.00 43.69 3.42
116 117 2.603473 CACCACTCCTCACCCGGA 60.603 66.667 0.73 0.00 0.00 5.14
117 118 3.706373 CCACCACTCCTCACCCGG 61.706 72.222 0.00 0.00 0.00 5.73
118 119 4.394712 GCCACCACTCCTCACCCG 62.395 72.222 0.00 0.00 0.00 5.28
119 120 4.394712 CGCCACCACTCCTCACCC 62.395 72.222 0.00 0.00 0.00 4.61
120 121 3.626924 ACGCCACCACTCCTCACC 61.627 66.667 0.00 0.00 0.00 4.02
121 122 2.357517 CACGCCACCACTCCTCAC 60.358 66.667 0.00 0.00 0.00 3.51
122 123 3.625897 CCACGCCACCACTCCTCA 61.626 66.667 0.00 0.00 0.00 3.86
123 124 3.626924 ACCACGCCACCACTCCTC 61.627 66.667 0.00 0.00 0.00 3.71
124 125 3.941188 CACCACGCCACCACTCCT 61.941 66.667 0.00 0.00 0.00 3.69
130 131 4.699522 GAGTCCCACCACGCCACC 62.700 72.222 0.00 0.00 0.00 4.61
131 132 4.699522 GGAGTCCCACCACGCCAC 62.700 72.222 0.00 0.00 36.31 5.01
134 135 3.998672 TTCGGAGTCCCACCACGC 61.999 66.667 2.80 0.00 0.00 5.34
135 136 2.048503 GTTCGGAGTCCCACCACG 60.049 66.667 2.80 0.00 0.00 4.94
136 137 1.004918 CTGTTCGGAGTCCCACCAC 60.005 63.158 2.80 0.00 0.00 4.16
137 138 2.214216 CCTGTTCGGAGTCCCACCA 61.214 63.158 2.80 0.00 33.16 4.17
138 139 2.663196 CCTGTTCGGAGTCCCACC 59.337 66.667 2.80 0.00 33.16 4.61
139 140 2.168666 GACCCTGTTCGGAGTCCCAC 62.169 65.000 2.80 1.09 33.16 4.61
140 141 1.911766 GACCCTGTTCGGAGTCCCA 60.912 63.158 2.80 0.00 33.16 4.37
141 142 0.324091 TAGACCCTGTTCGGAGTCCC 60.324 60.000 2.80 0.00 35.04 4.46
142 143 1.477295 CTTAGACCCTGTTCGGAGTCC 59.523 57.143 0.00 0.00 35.04 3.85
143 144 2.169330 ACTTAGACCCTGTTCGGAGTC 58.831 52.381 0.00 0.00 34.83 3.36
144 145 2.305858 ACTTAGACCCTGTTCGGAGT 57.694 50.000 0.00 0.00 33.16 3.85
145 146 3.326747 CAAACTTAGACCCTGTTCGGAG 58.673 50.000 0.00 0.00 33.16 4.63
146 147 2.549349 GCAAACTTAGACCCTGTTCGGA 60.549 50.000 0.00 0.00 33.16 4.55
147 148 1.804748 GCAAACTTAGACCCTGTTCGG 59.195 52.381 0.00 0.00 0.00 4.30
148 149 1.804748 GGCAAACTTAGACCCTGTTCG 59.195 52.381 0.00 0.00 0.00 3.95
149 150 1.804748 CGGCAAACTTAGACCCTGTTC 59.195 52.381 0.00 0.00 0.00 3.18
150 151 1.544759 CCGGCAAACTTAGACCCTGTT 60.545 52.381 0.00 0.00 0.00 3.16
151 152 0.036306 CCGGCAAACTTAGACCCTGT 59.964 55.000 0.00 0.00 0.00 4.00
152 153 0.323629 TCCGGCAAACTTAGACCCTG 59.676 55.000 0.00 0.00 0.00 4.45
153 154 1.003233 CTTCCGGCAAACTTAGACCCT 59.997 52.381 0.00 0.00 0.00 4.34
154 155 1.002773 TCTTCCGGCAAACTTAGACCC 59.997 52.381 0.00 0.00 0.00 4.46
155 156 2.467566 TCTTCCGGCAAACTTAGACC 57.532 50.000 0.00 0.00 0.00 3.85
156 157 4.275196 AGTTTTCTTCCGGCAAACTTAGAC 59.725 41.667 12.48 1.57 37.44 2.59
157 158 4.457466 AGTTTTCTTCCGGCAAACTTAGA 58.543 39.130 12.48 0.00 37.44 2.10
158 159 4.515567 AGAGTTTTCTTCCGGCAAACTTAG 59.484 41.667 16.93 0.00 40.15 2.18
159 160 4.457466 AGAGTTTTCTTCCGGCAAACTTA 58.543 39.130 16.93 0.00 40.15 2.24
160 161 3.288092 AGAGTTTTCTTCCGGCAAACTT 58.712 40.909 16.93 8.56 40.15 2.66
161 162 2.932261 AGAGTTTTCTTCCGGCAAACT 58.068 42.857 16.22 16.22 42.23 2.66
162 163 3.710326 AAGAGTTTTCTTCCGGCAAAC 57.290 42.857 0.00 3.40 39.46 2.93
163 164 4.729227 AAAAGAGTTTTCTTCCGGCAAA 57.271 36.364 0.00 0.00 42.80 3.68
164 165 4.678622 GAAAAAGAGTTTTCTTCCGGCAA 58.321 39.130 0.00 0.00 46.15 4.52
165 166 4.301637 GAAAAAGAGTTTTCTTCCGGCA 57.698 40.909 0.00 0.00 46.15 5.69
173 174 3.430333 TGCCCACGAAAAAGAGTTTTC 57.570 42.857 0.00 2.51 46.17 2.29
174 175 4.400529 AATGCCCACGAAAAAGAGTTTT 57.599 36.364 0.00 0.00 39.70 2.43
175 176 4.400529 AAATGCCCACGAAAAAGAGTTT 57.599 36.364 0.00 0.00 0.00 2.66
176 177 4.099419 AGAAAATGCCCACGAAAAAGAGTT 59.901 37.500 0.00 0.00 0.00 3.01
177 178 3.636764 AGAAAATGCCCACGAAAAAGAGT 59.363 39.130 0.00 0.00 0.00 3.24
178 179 3.983344 CAGAAAATGCCCACGAAAAAGAG 59.017 43.478 0.00 0.00 0.00 2.85
179 180 3.243704 CCAGAAAATGCCCACGAAAAAGA 60.244 43.478 0.00 0.00 0.00 2.52
180 181 3.059166 CCAGAAAATGCCCACGAAAAAG 58.941 45.455 0.00 0.00 0.00 2.27
181 182 2.224161 CCCAGAAAATGCCCACGAAAAA 60.224 45.455 0.00 0.00 0.00 1.94
182 183 1.342819 CCCAGAAAATGCCCACGAAAA 59.657 47.619 0.00 0.00 0.00 2.29
183 184 0.965439 CCCAGAAAATGCCCACGAAA 59.035 50.000 0.00 0.00 0.00 3.46
184 185 0.111446 TCCCAGAAAATGCCCACGAA 59.889 50.000 0.00 0.00 0.00 3.85
185 186 0.111446 TTCCCAGAAAATGCCCACGA 59.889 50.000 0.00 0.00 0.00 4.35
186 187 0.243636 GTTCCCAGAAAATGCCCACG 59.756 55.000 0.00 0.00 0.00 4.94
187 188 1.273327 CTGTTCCCAGAAAATGCCCAC 59.727 52.381 0.00 0.00 41.50 4.61
188 189 1.133199 ACTGTTCCCAGAAAATGCCCA 60.133 47.619 0.00 0.00 41.50 5.36
189 190 1.632589 ACTGTTCCCAGAAAATGCCC 58.367 50.000 0.00 0.00 41.50 5.36
190 191 3.131046 CCATACTGTTCCCAGAAAATGCC 59.869 47.826 0.00 0.00 41.50 4.40
191 192 3.763897 ACCATACTGTTCCCAGAAAATGC 59.236 43.478 0.00 0.00 41.50 3.56
192 193 5.713025 CAACCATACTGTTCCCAGAAAATG 58.287 41.667 0.00 0.00 41.50 2.32
193 194 4.220602 GCAACCATACTGTTCCCAGAAAAT 59.779 41.667 0.00 0.00 41.50 1.82
194 195 3.572255 GCAACCATACTGTTCCCAGAAAA 59.428 43.478 0.00 0.00 41.50 2.29
195 196 3.153919 GCAACCATACTGTTCCCAGAAA 58.846 45.455 0.00 0.00 41.50 2.52
196 197 2.375174 AGCAACCATACTGTTCCCAGAA 59.625 45.455 0.00 0.00 41.50 3.02
197 198 1.985159 AGCAACCATACTGTTCCCAGA 59.015 47.619 0.00 0.00 41.50 3.86
198 199 2.290260 TGAGCAACCATACTGTTCCCAG 60.290 50.000 0.00 0.00 44.68 4.45
199 200 1.702401 TGAGCAACCATACTGTTCCCA 59.298 47.619 0.00 0.00 0.00 4.37
200 201 2.489938 TGAGCAACCATACTGTTCCC 57.510 50.000 0.00 0.00 0.00 3.97
201 202 4.757149 GGATATGAGCAACCATACTGTTCC 59.243 45.833 0.00 0.00 32.45 3.62
202 203 5.368145 TGGATATGAGCAACCATACTGTTC 58.632 41.667 0.00 0.00 32.45 3.18
203 204 5.372343 TGGATATGAGCAACCATACTGTT 57.628 39.130 0.00 0.00 32.45 3.16
207 208 9.066892 TCTAAATTTGGATATGAGCAACCATAC 57.933 33.333 0.00 0.00 32.45 2.39
210 211 7.118723 ACTCTAAATTTGGATATGAGCAACCA 58.881 34.615 4.56 0.00 0.00 3.67
298 302 1.686052 AGAAATTGCGCACCAAAAGGA 59.314 42.857 11.12 0.00 36.92 3.36
299 303 1.794116 CAGAAATTGCGCACCAAAAGG 59.206 47.619 11.12 0.00 36.92 3.11
305 309 0.532115 AATCCCAGAAATTGCGCACC 59.468 50.000 11.12 0.00 0.00 5.01
421 431 1.342819 GGTGAGTGAGTGAAGCAGACT 59.657 52.381 0.00 0.00 0.00 3.24
425 435 1.486310 AGTTGGTGAGTGAGTGAAGCA 59.514 47.619 0.00 0.00 0.00 3.91
473 483 4.865761 TGCGGCCGCGATGTACTC 62.866 66.667 41.73 15.97 45.51 2.59
535 566 1.148310 CAAGTGTACGTCAAGGCAGG 58.852 55.000 0.00 0.00 0.00 4.85
569 600 3.154827 TGGTGGCCTTTTTCTTCTAGG 57.845 47.619 3.32 0.00 0.00 3.02
570 601 3.057245 GCTTGGTGGCCTTTTTCTTCTAG 60.057 47.826 3.32 0.00 0.00 2.43
675 893 3.826157 AGAGAGAGAAACAGAGTGTGAGG 59.174 47.826 0.00 0.00 0.00 3.86
712 934 2.292267 GGTGCTCTCTCTCTCTCTCTG 58.708 57.143 0.00 0.00 0.00 3.35
771 995 0.178873 AGGGTAGGGTTCTTGCTCCA 60.179 55.000 0.00 0.00 0.00 3.86
800 1024 2.622942 GTTTGCTTGTGTCCTCCATGAA 59.377 45.455 0.00 0.00 0.00 2.57
828 1052 4.322650 CCCTCTCTCTTCCTCAAAACTCTG 60.323 50.000 0.00 0.00 0.00 3.35
847 1071 1.621992 TCTCTCTCACACACACCCTC 58.378 55.000 0.00 0.00 0.00 4.30
850 1074 2.564947 AGGATTCTCTCTCACACACACC 59.435 50.000 0.00 0.00 0.00 4.16
852 1076 4.923415 TCTAGGATTCTCTCTCACACACA 58.077 43.478 0.00 0.00 0.00 3.72
854 1078 5.190726 TCTCTCTAGGATTCTCTCTCACACA 59.809 44.000 0.00 0.00 0.00 3.72
855 1079 5.680619 TCTCTCTAGGATTCTCTCTCACAC 58.319 45.833 0.00 0.00 0.00 3.82
856 1080 5.665360 TCTCTCTCTAGGATTCTCTCTCACA 59.335 44.000 0.00 0.00 0.00 3.58
857 1081 6.174720 TCTCTCTCTAGGATTCTCTCTCAC 57.825 45.833 0.00 0.00 0.00 3.51
858 1082 5.905331 ACTCTCTCTCTAGGATTCTCTCTCA 59.095 44.000 0.00 0.00 0.00 3.27
882 1106 0.251519 TGAGGCAGCTCTCACTCTCA 60.252 55.000 8.95 1.10 38.70 3.27
894 1118 1.651240 CGGCAATGGAACTGAGGCAG 61.651 60.000 0.00 0.00 37.52 4.85
895 1119 1.675310 CGGCAATGGAACTGAGGCA 60.675 57.895 0.00 0.00 0.00 4.75
902 1156 2.158957 TCTATGGAGACGGCAATGGAAC 60.159 50.000 0.00 0.00 0.00 3.62
913 1167 5.473305 GCGACGACGATCTCTATGGAGAC 62.473 56.522 11.42 4.96 43.99 3.36
1099 1358 2.203938 GGTGGTGGAGGTGGAGGA 60.204 66.667 0.00 0.00 0.00 3.71
1263 1537 3.194861 CGACTGGAAAGTCACTGAAACA 58.805 45.455 6.68 0.00 38.65 2.83
1266 1540 1.760613 ACCGACTGGAAAGTCACTGAA 59.239 47.619 6.68 0.00 38.65 3.02
1269 1543 0.680061 GGACCGACTGGAAAGTCACT 59.320 55.000 6.68 0.00 38.65 3.41
1272 1546 0.320508 GGTGGACCGACTGGAAAGTC 60.321 60.000 0.00 0.00 39.21 3.01
1275 1549 1.812686 CGAGGTGGACCGACTGGAAA 61.813 60.000 0.00 0.00 42.08 3.13
1659 1933 4.880426 GGGATGGGGCCGGAGAGA 62.880 72.222 5.05 0.00 0.00 3.10
1671 1945 0.036765 TGGAAAACGAGTCGGGGATG 60.037 55.000 18.30 0.00 0.00 3.51
1686 1960 0.321671 CGAGGTTGGAGAGCTTGGAA 59.678 55.000 0.00 0.00 35.91 3.53
1834 2108 2.904866 GGTGAGGTTGGCGCACAA 60.905 61.111 10.83 8.61 36.54 3.33
1986 2260 1.634225 GTCGAGCGAGACGAGAGAG 59.366 63.158 0.00 0.00 40.37 3.20
2092 2366 3.014538 TGGGATGGTGCCGGTGAT 61.015 61.111 1.90 0.00 0.00 3.06
2988 3270 1.255667 TGACGAGGTTGTCTAGCCCC 61.256 60.000 0.00 0.00 39.64 5.80
2994 3276 0.469331 TGAGGGTGACGAGGTTGTCT 60.469 55.000 0.00 0.00 39.64 3.41
3291 3576 2.946346 GCCACCACCATTGCCCTTG 61.946 63.158 0.00 0.00 0.00 3.61
3298 3583 4.740822 GCTCCCGCCACCACCATT 62.741 66.667 0.00 0.00 0.00 3.16
3408 3693 4.680237 TTGGCGTCGACCAGGCTG 62.680 66.667 10.58 7.75 41.82 4.85
3612 3897 2.818714 CAGCAGCAGCCGAGGAAG 60.819 66.667 0.00 0.00 43.56 3.46
3717 4023 2.524394 ACGTCCCACTCCAGCTGT 60.524 61.111 13.81 0.00 0.00 4.40
3988 4294 0.603569 GAGTCATATCGGACCGGCAT 59.396 55.000 15.25 3.44 38.59 4.40
4043 4533 3.257393 TGCACACAATCAAACACCAAAC 58.743 40.909 0.00 0.00 0.00 2.93
4071 4581 9.896645 ATGATAAATAATTCGACCTCTGCATAT 57.103 29.630 0.00 0.00 0.00 1.78
4161 4671 4.202409 TGTTCATAGATGGTGTGTTGGACA 60.202 41.667 0.00 0.00 0.00 4.02
4232 4743 1.402259 TCGCTCTTCTCGGTGATCTTC 59.598 52.381 0.00 0.00 0.00 2.87
4292 4803 4.207281 TCGATCGGCTGCTTCCCG 62.207 66.667 16.41 4.26 46.88 5.14
4400 4911 0.972983 CCTCCACCTCTGTGTCGGAT 60.973 60.000 0.00 0.00 41.09 4.18
4409 4920 0.908198 GCAACATCTCCTCCACCTCT 59.092 55.000 0.00 0.00 0.00 3.69
4425 4936 2.672651 CACGCCCATGACCTGCAA 60.673 61.111 0.00 0.00 0.00 4.08
4897 5435 8.797266 AAAAAGCCTTAGTTTTCGTTCTAATG 57.203 30.769 0.00 0.00 0.00 1.90
4905 5443 8.647226 CCATCAAATAAAAAGCCTTAGTTTTCG 58.353 33.333 0.00 0.00 0.00 3.46
4922 5460 4.032960 ACACAGAAGGCACCATCAAATA 57.967 40.909 0.00 0.00 0.00 1.40
5013 5551 3.191669 CAGTGAAGTAACGTGGACAACA 58.808 45.455 0.00 0.00 0.00 3.33
5014 5552 2.542595 CCAGTGAAGTAACGTGGACAAC 59.457 50.000 0.00 0.00 0.00 3.32
5015 5553 2.168936 ACCAGTGAAGTAACGTGGACAA 59.831 45.455 0.00 0.00 32.26 3.18
5022 5560 2.286772 GCCAAACACCAGTGAAGTAACG 60.287 50.000 4.48 0.00 0.00 3.18
5026 5564 1.064758 TCTGCCAAACACCAGTGAAGT 60.065 47.619 4.48 0.00 0.00 3.01
5276 5879 7.334421 CCATTAAACACTACTAGCTCAACACAT 59.666 37.037 0.00 0.00 0.00 3.21
5302 5905 2.158971 GCCAGGACTCCTTGAGATCTTC 60.159 54.545 0.00 0.00 33.32 2.87
5350 5953 8.019656 TCCAGTTTACTCAGAAGAAACTTAGT 57.980 34.615 6.62 0.00 40.54 2.24
5360 5963 5.607939 TGTTGTCTCCAGTTTACTCAGAA 57.392 39.130 0.00 0.00 0.00 3.02
5392 5995 7.288560 ACTCTAGTTCCTATGAAATCCGTCTA 58.711 38.462 0.00 0.00 30.29 2.59
5457 6060 8.853345 GTCATGCAAATCAAACAAACTATGTAG 58.147 33.333 0.00 0.00 42.99 2.74
5495 6098 7.828712 AGTATTCTAATGGCTTAGATCGTACC 58.171 38.462 7.08 0.00 42.22 3.34
5513 6116 8.883731 CGGTTATTTCAAGTTGATGAGTATTCT 58.116 33.333 6.36 0.00 0.00 2.40
5541 6144 2.949909 AACCACGCGATAGGTGCCA 61.950 57.895 15.93 0.00 38.37 4.92
5606 6209 7.025963 AGAATGAGATTTGAGCGAATGAAAAC 58.974 34.615 0.00 0.00 0.00 2.43
5666 6269 4.892345 TGGAACCACATGAACTTGAATCAA 59.108 37.500 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.