Locus 4107

Sequence ID	2L_DroMel_CAF1
Location	11,802,276 – 11,802,502
Length	226
Max. P	0.999925

overview

Window 1

Location	11,802,276 – 11,802,382
Length	106
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	100.00
Mean single sequence MFE	-29.72
Consensus MFE	-29.72
Energy contribution	-29.72
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.12
Structure conservation index	1.00
SVM decision value	1.52
SVM RNA-class probability	0.960680
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11802276 106 + 22407834
UCACACUCACCAGUGUGCCACAUGUAGUGGUUAACAUAGUGUUCCUUGCGCGUAAAGGACUUCUUACAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGC
.((.((.(((..(((((((((((((.(((((......((...(((((.......)))))...)).......))))).)).))))))))...)))..))).)).)). ( -29.72)
>DroSec_CAF1 9630 106 + 1
UCACACUCACCAGUGUGCCACAUGUAGUGGUUAACAUAGUGUUCCUUGCGCGUAAAGGACUUCUUACAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGC
.((.((.(((..(((((((((((((.(((((......((...(((((.......)))))...)).......))))).)).))))))))...)))..))).)).)). ( -29.72)
>DroSim_CAF1 9623 106 + 1
UCACACUCACCAGUGUGCCACAUGUAGUGGUUAACAUAGUGUUCCUUGCGCGUAAAGGACUUCUUACAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGC
.((.((.(((..(((((((((((((.(((((......((...(((((.......)))))...)).......))))).)).))))))))...)))..))).)).)). ( -29.72)
>DroWil_CAF1 14675 106 + 1
UCACACUCACCAGUGUGCCACAUGUAGUGGUUAACAUAGUGUUCCUUGCGCGUAAAGGACUUCUUACAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGC
.((.((.(((..(((((((((((((.(((((......((...(((((.......)))))...)).......))))).)).))))))))...)))..))).)).)). ( -29.72)
>DroYak_CAF1 9535 106 + 1
UCACACUCACCAGUGUGCCACAUGUAGUGGUUAACAUAGUGUUCCUUGCGCGUAAAGGACUUCUUACAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGC
.((.((.(((..(((((((((((((.(((((......((...(((((.......)))))...)).......))))).)).))))))))...)))..))).)).)). ( -29.72)
>DroPer_CAF1 13835 106 + 1
UCACACUCACCAGUGUGCCACAUGUAGUGGUUAACAUAGUGUUCCUUGCGCGUAAAGGACUUCUUACAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGC
.((.((.(((..(((((((((((((.(((((......((...(((((.......)))))...)).......))))).)).))))))))...)))..))).)).)). ( -29.72)
>consensus
UCACACUCACCAGUGUGCCACAUGUAGUGGUUAACAUAGUGUUCCUUGCGCGUAAAGGACUUCUUACAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGC
.((.((.(((..(((((((((((((.(((((......((...(((((.......)))))...)).......))))).)).))))))))...)))..))).)).)). (-29.72 = -29.72 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	11,802,276 – 11,802,382
Length	106
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	100.00
Mean single sequence MFE	-31.30
Consensus MFE	-31.30
Energy contribution	-31.30
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.36
Structure conservation index	1.00
SVM decision value	2.21
SVM RNA-class probability	0.990389
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11802276 106 - 22407834
GCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUGUAAGAAGUCCUUUACGCGCAAGGAACACUAUGUUAACCACUACAUGUGGCACACUGGUGAGUGUGA
.....(((((.((((...))))...((.(((((.....((((((......))))))))))).)).((((((((...((((.....)))).))).))))).))))). ( -31.30)
>DroSec_CAF1 9630 106 - 1
GCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUGUAAGAAGUCCUUUACGCGCAAGGAACACUAUGUUAACCACUACAUGUGGCACACUGGUGAGUGUGA
.....(((((.((((...))))...((.(((((.....((((((......))))))))))).)).((((((((...((((.....)))).))).))))).))))). ( -31.30)
>DroSim_CAF1 9623 106 - 1
GCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUGUAAGAAGUCCUUUACGCGCAAGGAACACUAUGUUAACCACUACAUGUGGCACACUGGUGAGUGUGA
.....(((((.((((...))))...((.(((((.....((((((......))))))))))).)).((((((((...((((.....)))).))).))))).))))). ( -31.30)
>DroWil_CAF1 14675 106 - 1
GCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUGUAAGAAGUCCUUUACGCGCAAGGAACACUAUGUUAACCACUACAUGUGGCACACUGGUGAGUGUGA
.....(((((.((((...))))...((.(((((.....((((((......))))))))))).)).((((((((...((((.....)))).))).))))).))))). ( -31.30)
>DroYak_CAF1 9535 106 - 1
GCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUGUAAGAAGUCCUUUACGCGCAAGGAACACUAUGUUAACCACUACAUGUGGCACACUGGUGAGUGUGA
.....(((((.((((...))))...((.(((((.....((((((......))))))))))).)).((((((((...((((.....)))).))).))))).))))). ( -31.30)
>DroPer_CAF1 13835 106 - 1
GCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUGUAAGAAGUCCUUUACGCGCAAGGAACACUAUGUUAACCACUACAUGUGGCACACUGGUGAGUGUGA
.....(((((.((((...))))...((.(((((.....((((((......))))))))))).)).((((((((...((((.....)))).))).))))).))))). ( -31.30)
>consensus
GCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUGUAAGAAGUCCUUUACGCGCAAGGAACACUAUGUUAACCACUACAUGUGGCACACUGGUGAGUGUGA
.....(((((.((((...))))...((.(((((.....((((((......))))))))))).)).((((((((...((((.....)))).))).))))).))))). (-31.30 = -31.30 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	11,802,302 – 11,802,422
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	98.72
Mean single sequence MFE	-38.35
Consensus MFE	-34.95
Energy contribution	-35.12
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.54
Structure conservation index	0.91
SVM decision value	1.21
SVM RNA-class probability	0.931680
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11802302 120 + 22407834
GUGGUUAACAUAGUGUUCCUUGCGCGUAAAGGACUUCUUACAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGCGCACAUGGUUGACCAUGUGCUCCUUGCGCGUGAACGUCUU
(((.....)))(((((((...((((((((.(((...............((((..(..(((.(.....))))..)..))))((((((((....)))))))))))))))))))))))).)). ( -41.60)
>DroPse_CAF1 13712 120 + 1
GUGGUUAACAUAGUGUUCCUUGCGCGUAAAGGACUUCUUACAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGCGCACAUGGUUAACCAUAUGCUCCUUGCGCGUGAACGUCUU
(((.....)))(((((((...((((((((.(((...............((((..(..(((.(.....))))..)..))))(((.((((....)))).))))))))))))))))))).)). ( -35.60)
>DroSim_CAF1 9649 120 + 1
GUGGUUAACAUAGUGUUCCUUGCGCGUAAAGGACUUCUUACAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGCGCACAUGGUUGACCAUGUGCUCCUUGCGCGUGAACGUCUU
(((.....)))(((((((...((((((((.(((...............((((..(..(((.(.....))))..)..))))((((((((....)))))))))))))))))))))))).)). ( -41.60)
>DroWil_CAF1 14701 120 + 1
GUGGUUAACAUAGUGUUCCUUGCGCGUAAAGGACUUCUUACAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGCGCACAUGGUUAACCAUAUGCUCCUUGCGCGUAAACGUCUU
(((.....)))........((((((((((.(((...............((((..(..(((.(.....))))..)..))))(((.((((....)))).))))))))))))))))....... ( -34.10)
>DroYak_CAF1 9561 120 + 1
GUGGUUAACAUAGUGUUCCUUGCGCGUAAAGGACUUCUUACAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGCGCACAUGGUUGACCAUGUGCUCCUUGCGCGUGAACGUCUU
(((.....)))(((((((...((((((((.(((...............((((..(..(((.(.....))))..)..))))((((((((....)))))))))))))))))))))))).)). ( -41.60)
>DroPer_CAF1 13861 120 + 1
GUGGUUAACAUAGUGUUCCUUGCGCGUAAAGGACUUCUUACAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGCGCACAUGGUUAACCAUAUGCUCCUUGCGCGUGAACGUCUU
(((.....)))(((((((...((((((((.(((...............((((..(..(((.(.....))))..)..))))(((.((((....)))).))))))))))))))))))).)). ( -35.60)
>consensus
GUGGUUAACAUAGUGUUCCUUGCGCGUAAAGGACUUCUUACAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGCGCACAUGGUUAACCAUAUGCUCCUUGCGCGUGAACGUCUU
(((.....)))(((((((...((((((((.(((...............((((..(..(((.(.....))))..)..))))(((.((((....)))).))))))))))))))))))).)). (-34.95 = -35.12 +   0.17)

alignment

secondary structure

dotplot

Window 4

Location	11,802,302 – 11,802,422
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	98.72
Mean single sequence MFE	-37.77
Consensus MFE	-38.16
Energy contribution	-37.77
Covariance contribution	-0.39
Combinations/Pair	1.07
Mean z-score	-2.21
Structure conservation index	1.01
SVM decision value	4.59
SVM RNA-class probability	0.999925
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11802302 120 - 22407834
AAGACGUUCACGCGCAAGGAGCACAUGGUCAACCAUGUGCGCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUGUAAGAAGUCCUUUACGCGCAAGGAACACUAUGUUAACCAC
.....((((..(((((((((((((((((....))))))))((((.......((((...))))......))))...............)))))...))))...)))).............. ( -39.02)
>DroPse_CAF1 13712 120 - 1
AAGACGUUCACGCGCAAGGAGCAUAUGGUUAACCAUGUGCGCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUGUAAGAAGUCCUUUACGCGCAAGGAACACUAUGUUAACCAC
.....((((..(((((((((((((((((....))))))))((((.......((((...))))......))))...............)))))...))))...)))).............. ( -37.12)
>DroSim_CAF1 9649 120 - 1
AAGACGUUCACGCGCAAGGAGCACAUGGUCAACCAUGUGCGCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUGUAAGAAGUCCUUUACGCGCAAGGAACACUAUGUUAACCAC
.....((((..(((((((((((((((((....))))))))((((.......((((...))))......))))...............)))))...))))...)))).............. ( -39.02)
>DroWil_CAF1 14701 120 - 1
AAGACGUUUACGCGCAAGGAGCAUAUGGUUAACCAUGUGCGCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUGUAAGAAGUCCUUUACGCGCAAGGAACACUAUGUUAACCAC
.....((((..(((((((((((((((((....))))))))((((.......((((...))))......))))...............)))))...))))...)))).............. ( -35.32)
>DroYak_CAF1 9561 120 - 1
AAGACGUUCACGCGCAAGGAGCACAUGGUCAACCAUGUGCGCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUGUAAGAAGUCCUUUACGCGCAAGGAACACUAUGUUAACCAC
.....((((..(((((((((((((((((....))))))))((((.......((((...))))......))))...............)))))...))))...)))).............. ( -39.02)
>DroPer_CAF1 13861 120 - 1
AAGACGUUCACGCGCAAGGAGCAUAUGGUUAACCAUGUGCGCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUGUAAGAAGUCCUUUACGCGCAAGGAACACUAUGUUAACCAC
.....((((..(((((((((((((((((....))))))))((((.......((((...))))......))))...............)))))...))))...)))).............. ( -37.12)
>consensus
AAGACGUUCACGCGCAAGGAGCACAUGGUCAACCAUGUGCGCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUGUAAGAAGUCCUUUACGCGCAAGGAACACUAUGUUAACCAC
.....((((..(((((((((((((((((....))))))))((((.......((((...))))......))))...............)))))...))))...)))).............. (-38.16 = -37.77 +  -0.39)

alignment

secondary structure

dotplot

Window 5

Location	11,802,342 – 11,802,462
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	98.44
Mean single sequence MFE	-46.28
Consensus MFE	-42.48
Energy contribution	-42.65
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.33
Structure conservation index	0.92
SVM decision value	0.89
SVM RNA-class probability	0.876374
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11802342 120 + 22407834
CAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGCGCACAUGGUUGACCAUGUGCUCCUUGCGCGUGAACGUCUUGGCGCAGUACUGGCAACGGAAGGGCGUUUCGCCCGUGUGC
(((((((((...))))))(((((.(((.((((((((....)))))))).))).(((((((.....))))))).))))))))(((((...(((....)))..(((((...))))).))))) ( -49.60)
>DroPse_CAF1 13752 120 + 1
CAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGCGCACAUGGUUAACCAUAUGCUCCUUGCGCGUGAACGUCUUGGCGCAGUACUGGCAACGGAAGGGCGUUUCGCCCGUGUGC
(((((((((...))))))(((((.((((((((((((....))))))))..........((.....))..))))))))))))(((((...(((....)))..(((((...))))).))))) ( -43.50)
>DroSim_CAF1 9689 120 + 1
CAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGCGCACAUGGUUGACCAUGUGCUCCUUGCGCGUGAACGUCUUGGCGCAGUACUGGCAACGGAAGGGCGUUUCGCCCGUGUGC
(((((((((...))))))(((((.(((.((((((((....)))))))).))).(((((((.....))))))).))))))))(((((...(((....)))..(((((...))))).))))) ( -49.60)
>DroWil_CAF1 14741 120 + 1
CAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGCGCACAUGGUUAACCAUAUGCUCCUUGCGCGUAAACGUCUUUGCGCAGUACUGGCAACGGAAGGGCGUUUCGCCCGUGUGC
........((((..(..(((.(.....))))..)..))))((((((((..........((.....))(((.((((((((((.((..((....))..)).))))))))))))))))))))) ( -41.90)
>DroYak_CAF1 9601 120 + 1
CAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGCGCACAUGGUUGACCAUGUGCUCCUUGCGCGUGAACGUCUUGGCGCAGUACUGGCAACGGAAGGGCGUUUCGCCCGUGUGC
(((((((((...))))))(((((.(((.((((((((....)))))))).))).(((((((.....))))))).))))))))(((((...(((....)))..(((((...))))).))))) ( -49.60)
>DroPer_CAF1 13901 120 + 1
CAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGCGCACAUGGUUAACCAUAUGCUCCUUGCGCGUGAACGUCUUGGCGCAGUACUGGCAACGGAAGGGCGUUUCGCCCGUGUGC
(((((((((...))))))(((((.((((((((((((....))))))))..........((.....))..))))))))))))(((((...(((....)))..(((((...))))).))))) ( -43.50)
>consensus
CAAAUAUCGCAACGAUGUGGCGUCUCACCCGUGUGUUUGCGCACAUGGUUAACCAUAUGCUCCUUGCGCGUGAACGUCUUGGCGCAGUACUGGCAACGGAAGGGCGUUUCGCCCGUGUGC
...((((((...))))))(((((.((((((((((((....))))))))..........((.....))..)))))))))...(((((...(((....)))..(((((...))))).))))) (-42.48 = -42.65 +   0.17)

alignment

secondary structure

dotplot

Window 6

Location	11,802,342 – 11,802,462
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	98.44
Mean single sequence MFE	-42.80
Consensus MFE	-42.90
Energy contribution	-42.65
Covariance contribution	-0.25
Combinations/Pair	1.03
Mean z-score	-1.44
Structure conservation index	1.00
SVM decision value	2.71
SVM RNA-class probability	0.996535
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11802342 120 - 22407834
GCACACGGGCGAAACGCCCUUCCGUUGCCAGUACUGCGCCAAGACGUUCACGCGCAAGGAGCACAUGGUCAACCAUGUGCGCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUG
(((.(((((((...(((((.....((((......(((((............)))))....((((((((....))))))))))))......)))))...))))....))))))........ ( -43.50)
>DroPse_CAF1 13752 120 - 1
GCACACGGGCGAAACGCCCUUCCGUUGCCAGUACUGCGCCAAGACGUUCACGCGCAAGGAGCAUAUGGUUAACCAUGUGCGCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUG
(((.(((((((...(((((.....((((......(((((............)))))....((((((((....))))))))))))......)))))...))))....))))))........ ( -41.60)
>DroSim_CAF1 9689 120 - 1
GCACACGGGCGAAACGCCCUUCCGUUGCCAGUACUGCGCCAAGACGUUCACGCGCAAGGAGCACAUGGUCAACCAUGUGCGCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUG
(((.(((((((...(((((.....((((......(((((............)))))....((((((((....))))))))))))......)))))...))))....))))))........ ( -43.50)
>DroWil_CAF1 14741 120 - 1
GCACACGGGCGAAACGCCCUUCCGUUGCCAGUACUGCGCAAAGACGUUUACGCGCAAGGAGCAUAUGGUUAACCAUGUGCGCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUG
(((.(((((((...(((((.(((.((((..(((..(((......))).)))..)))))))((((((((....))))))))..........)))))...))))....))))))........ ( -43.10)
>DroYak_CAF1 9601 120 - 1
GCACACGGGCGAAACGCCCUUCCGUUGCCAGUACUGCGCCAAGACGUUCACGCGCAAGGAGCACAUGGUCAACCAUGUGCGCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUG
(((.(((((((...(((((.....((((......(((((............)))))....((((((((....))))))))))))......)))))...))))....))))))........ ( -43.50)
>DroPer_CAF1 13901 120 - 1
GCACACGGGCGAAACGCCCUUCCGUUGCCAGUACUGCGCCAAGACGUUCACGCGCAAGGAGCAUAUGGUUAACCAUGUGCGCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUG
(((.(((((((...(((((.....((((......(((((............)))))....((((((((....))))))))))))......)))))...))))....))))))........ ( -41.60)
>consensus
GCACACGGGCGAAACGCCCUUCCGUUGCCAGUACUGCGCCAAGACGUUCACGCGCAAGGAGCACAUGGUCAACCAUGUGCGCAAACACACGGGUGAGACGCCACAUCGUUGCGAUAUUUG
(((.(((((((...(((((.....((((......(((((............)))))....((((((((....))))))))))))......)))))...))))....))))))........ (-42.90 = -42.65 +  -0.25)

alignment

secondary structure

dotplot

Window 7

Location	11,802,382 – 11,802,502
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	96.83
Mean single sequence MFE	-49.78
Consensus MFE	-43.93
Energy contribution	-44.02
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.98
Structure conservation index	0.88
SVM decision value	1.57
SVM RNA-class probability	0.965007
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11802382 120 + 22407834
GCACAUGGUUGACCAUGUGCUCCUUGCGCGUGAACGUCUUGGCGCAGUACUGGCAACGGAAGGGCGUUUCGCCCGUGUGCGAGCGGAAGUGAUUGUCCAGAUGCUCUUUGCGGGCAAAGG
((((((((....)))))))).((((((.((..(((((((.((((((...(((....)))..(((((...)))))...)))..((....))....))).)))))...))..)).)).)))) ( -53.40)
>DroPse_CAF1 13792 120 + 1
GCACAUGGUUAACCAUAUGCUCCUUGCGCGUGAACGUCUUGGCGCAGUACUGGCAACGGAAGGGCGUUUCGCCCGUGUGCGAGCGAAAGUGAUUGUCCAGAUGCUCUUUGCGGGCAAAGG
(((.((((....)))).))).((((((.((..(((((((.((((((...(((....)))..(((((...)))))...)))..((....))....))).)))))...))..)).)).)))) ( -47.40)
>DroSim_CAF1 9729 120 + 1
GCACAUGGUUGACCAUGUGCUCCUUGCGCGUGAACGUCUUGGCGCAGUACUGGCAACGGAAGGGCGUUUCGCCCGUGUGCGAGCGGAAGUGAUUGUCCAGAUGCUCUUUGCGGGCAAAGG
((((((((....)))))))).((((((.((..(((((((.((((((...(((....)))..(((((...)))))...)))..((....))....))).)))))...))..)).)).)))) ( -53.40)
>DroWil_CAF1 14781 120 + 1
GCACAUGGUUAACCAUAUGCUCCUUGCGCGUAAACGUCUUUGCGCAGUACUGGCAACGGAAGGGCGUUUCGCCCGUGUGCGAACGAAAAUGAUUGUCCAGAUGCUCUUUGCGGGCAAAUG
(((.((((....)))).)))...((((.((((((((((((((((((...(((....)))..(((((...))))).)))))))((((......))))..)))))...)))))).))))... ( -44.10)
>DroYak_CAF1 9641 120 + 1
GCACAUGGUUGACCAUGUGCUCCUUGCGCGUGAACGUCUUGGCGCAGUACUGGCAACGGAAGGGCGUUUCGCCCGUGUGCGAGCGGAAGUGAUUGUCCAGGUGCUCUUUGCGGGCAAAGG
((((((((....)))))))).((((((.((..((.(((((((((((...(((....)))..(((((...)))))...)))).((....))......))))).))..))..)).)).)))) ( -53.00)
>DroPer_CAF1 13941 120 + 1
GCACAUGGUUAACCAUAUGCUCCUUGCGCGUGAACGUCUUGGCGCAGUACUGGCAACGGAAGGGCGUUUCGCCCGUGUGCGAGCGAAAGUGAUUGUCCAGAUGCUCUUUGCGGGCAAAGG
(((.((((....)))).))).((((((.((..(((((((.((((((...(((....)))..(((((...)))))...)))..((....))....))).)))))...))..)).)).)))) ( -47.40)
>consensus
GCACAUGGUUAACCAUAUGCUCCUUGCGCGUGAACGUCUUGGCGCAGUACUGGCAACGGAAGGGCGUUUCGCCCGUGUGCGAGCGAAAGUGAUUGUCCAGAUGCUCUUUGCGGGCAAAGG
(((.((((....)))).))).((((((.(((((((((((.((((((...(((....)))..(((((...)))))...)))..((....))....))).)))))...)))))).)).)))) (-43.93 = -44.02 +   0.08)

alignment

secondary structure

dotplot

Window 8

Location	11,802,382 – 11,802,502
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	96.83
Mean single sequence MFE	-40.14
Consensus MFE	-39.07
Energy contribution	-38.43
Covariance contribution	-0.64
Combinations/Pair	1.09
Mean z-score	-1.66
Structure conservation index	0.97
SVM decision value	2.92
SVM RNA-class probability	0.997724
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11802382 120 - 22407834
CCUUUGCCCGCAAAGAGCAUCUGGACAAUCACUUCCGCUCGCACACGGGCGAAACGCCCUUCCGUUGCCAGUACUGCGCCAAGACGUUCACGCGCAAGGAGCACAUGGUCAACCAUGUGC
..((((((((....((((....(((........))))))).....)))))))).......(((.((((..((...(((......)))..))..)))))))((((((((....)))))))) ( -41.20)
>DroPse_CAF1 13792 120 - 1
CCUUUGCCCGCAAAGAGCAUCUGGACAAUCACUUUCGCUCGCACACGGGCGAAACGCCCUUCCGUUGCCAGUACUGCGCCAAGACGUUCACGCGCAAGGAGCAUAUGGUUAACCAUGUGC
.((((((.((....((((.((((((.......(((((((((....)))))))))......)))...((((....)).))..))).)))).)).)))))).((((((((....)))))))) ( -40.42)
>DroSim_CAF1 9729 120 - 1
CCUUUGCCCGCAAAGAGCAUCUGGACAAUCACUUCCGCUCGCACACGGGCGAAACGCCCUUCCGUUGCCAGUACUGCGCCAAGACGUUCACGCGCAAGGAGCACAUGGUCAACCAUGUGC
..((((((((....((((....(((........))))))).....)))))))).......(((.((((..((...(((......)))..))..)))))))((((((((....)))))))) ( -41.20)
>DroWil_CAF1 14781 120 - 1
CAUUUGCCCGCAAAGAGCAUCUGGACAAUCAUUUUCGUUCGCACACGGGCGAAACGCCCUUCCGUUGCCAGUACUGCGCAAAGACGUUUACGCGCAAGGAGCAUAUGGUUAACCAUGUGC
..((((((((....((((.....(.....)......)))).....)))))))).......(((.((((..(((..(((......))).)))..)))))))((((((((....)))))))) ( -36.40)
>DroYak_CAF1 9641 120 - 1
CCUUUGCCCGCAAAGAGCACCUGGACAAUCACUUCCGCUCGCACACGGGCGAAACGCCCUUCCGUUGCCAGUACUGCGCCAAGACGUUCACGCGCAAGGAGCACAUGGUCAACCAUGUGC
..((((((((....((((....(((........))))))).....)))))))).......(((.((((..((...(((......)))..))..)))))))((((((((....)))))))) ( -41.20)
>DroPer_CAF1 13941 120 - 1
CCUUUGCCCGCAAAGAGCAUCUGGACAAUCACUUUCGCUCGCACACGGGCGAAACGCCCUUCCGUUGCCAGUACUGCGCCAAGACGUUCACGCGCAAGGAGCAUAUGGUUAACCAUGUGC
.((((((.((....((((.((((((.......(((((((((....)))))))))......)))...((((....)).))..))).)))).)).)))))).((((((((....)))))))) ( -40.42)
>consensus
CCUUUGCCCGCAAAGAGCAUCUGGACAAUCACUUCCGCUCGCACACGGGCGAAACGCCCUUCCGUUGCCAGUACUGCGCCAAGACGUUCACGCGCAAGGAGCACAUGGUCAACCAUGUGC
..((((((((....((((....(((........))))))).....)))))))).......(((.((((..((...(((......)))..))..)))))))((((((((....)))))))) (-39.07 = -38.43 +  -0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:49 2006