Locus 4274

Sequence ID	3R_DroMel_CAF1
Location	11,401,640 – 11,401,836
Length	196
Max. P	0.999941

overview

Window 0

Location	11,401,640 – 11,401,756
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.77
Mean single sequence MFE	-23.52
Consensus MFE	-23.68
Energy contribution	-23.52
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-2.50
Structure conservation index	1.01
SVM decision value	4.71
SVM RNA-class probability	0.999941
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11401640 116 + 27905053
C----AUAUAUCUGCCCACUACCAAUUUUUAGUUUACGACUCUUCACAUUUUAAUGGCCAUCGCCACAAUCCGUUAAGAGUUGGAAUUUUAUUUCUCGUAAAAGAAAUACAAUUUGAGCA
.----..........................((((.((((((((.((.......((((....))))......)).))))))))(((((.(((((((......))))))).))))))))). ( -23.52)
>DroSec_CAF1 149303 119 + 1
CAUACAUAUAUCUGCCCACUACCAAUU-UUAGUUUACGACUCUUCACAUUUUAAUGGCCAUCGCCACAAUCCGUUAAGAGUUGGAAUUUUAUUUCUCGUAAAAGAAAUACAAUUUGAGCA
...........................-...((((.((((((((.((.......((((....))))......)).))))))))(((((.(((((((......))))))).))))))))). ( -23.52)
>DroSim_CAF1 140372 116 + 1
C----AUAUAUCUGCCCACUACCAAUUUUUAGUUUACGACUCUUCACAUUUUAAUGGCCAUCGCCACAAUCCGUUAAGAGUUGGAAUUUUAUUUCUCGUAAAAGAAAUACAAUUUGAGCA
.----..........................((((.((((((((.((.......((((....))))......)).))))))))(((((.(((((((......))))))).))))))))). ( -23.52)
>DroEre_CAF1 137388 115 + 1
-----AUAUGUCUGCCCACUACCAAUUUUUAGUUUACGACUCUUCACAUUUUAAUGGCCAUCGCCACAAUCCGUUAAGAGUUGGAGUUUUAUUUCUCGUAAAAGAAAUACAAUUUGAGCA
-----..........................((((.((((((((.((.......((((....))))......)).))))))))(((((.(((((((......))))))).))))))))). ( -23.52)
>DroYak_CAF1 140377 114 + 1
------UAUAUCUGCCCACUACCAAUUUUUAGUUUACGACUCUUCACAUUUUAAUGGCCAUCGCCACAAUCCGUUAAGAGUUGGAAUUUUAUUUCUCGUAAAAGAAAUACAAUUUGAGCA
------.........................((((.((((((((.((.......((((....))))......)).))))))))(((((.(((((((......))))))).))))))))). ( -23.52)
>consensus
C____AUAUAUCUGCCCACUACCAAUUUUUAGUUUACGACUCUUCACAUUUUAAUGGCCAUCGCCACAAUCCGUUAAGAGUUGGAAUUUUAUUUCUCGUAAAAGAAAUACAAUUUGAGCA
...............................((((.((((((((.((.......((((....))))......)).))))))))(((((.(((((((......))))))).))))))))). (-23.68 = -23.52 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	11,401,640 – 11,401,756
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.77
Mean single sequence MFE	-28.51
Consensus MFE	-27.70
Energy contribution	-27.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.12
Structure conservation index	0.97
SVM decision value	3.58
SVM RNA-class probability	0.999412
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11401640 116 - 27905053
UGCUCAAAUUGUAUUUCUUUUACGAGAAAUAAAAUUCCAACUCUUAACGGAUUGUGGCGAUGGCCAUUAAAAUGUGAAGAGUCGUAAACUAAAAAUUGGUAGUGGGCAGAUAUAU----G
((((((((((.((((((((....)))))))).))))...((((((.(((....(((((....))))).....))).)))))).....((((.....))))..)))))).......----. ( -28.30)
>DroSec_CAF1 149303 119 - 1
UGCUCAAAUUGUAUUUCUUUUACGAGAAAUAAAAUUCCAACUCUUAACGGAUUGUGGCGAUGGCCAUUAAAAUGUGAAGAGUCGUAAACUAA-AAUUGGUAGUGGGCAGAUAUAUGUAUG
((((((((((.((((((((....)))))))).))))...((((((.(((....(((((....))))).....))).)))))).....((((.-...))))..))))))............ ( -28.30)
>DroSim_CAF1 140372 116 - 1
UGCUCAAAUUGUAUUUCUUUUACGAGAAAUAAAAUUCCAACUCUUAACGGAUUGUGGCGAUGGCCAUUAAAAUGUGAAGAGUCGUAAACUAAAAAUUGGUAGUGGGCAGAUAUAU----G
((((((((((.((((((((....)))))))).))))...((((((.(((....(((((....))))).....))).)))))).....((((.....))))..)))))).......----. ( -28.30)
>DroEre_CAF1 137388 115 - 1
UGCUCAAAUUGUAUUUCUUUUACGAGAAAUAAAACUCCAACUCUUAACGGAUUGUGGCGAUGGCCAUUAAAAUGUGAAGAGUCGUAAACUAAAAAUUGGUAGUGGGCAGACAUAU-----
(((((......((((((((....))))))))..((((((((((((.(((....(((((....))))).....))).))))))..............))).)))))))).......----- ( -29.33)
>DroYak_CAF1 140377 114 - 1
UGCUCAAAUUGUAUUUCUUUUACGAGAAAUAAAAUUCCAACUCUUAACGGAUUGUGGCGAUGGCCAUUAAAAUGUGAAGAGUCGUAAACUAAAAAUUGGUAGUGGGCAGAUAUA------
((((((((((.((((((((....)))))))).))))...((((((.(((....(((((....))))).....))).)))))).....((((.....))))..))))))......------ ( -28.30)
>consensus
UGCUCAAAUUGUAUUUCUUUUACGAGAAAUAAAAUUCCAACUCUUAACGGAUUGUGGCGAUGGCCAUUAAAAUGUGAAGAGUCGUAAACUAAAAAUUGGUAGUGGGCAGAUAUAU____G
((((((.....((((((((....))))))))........((((((.(((....(((((....))))).....))).)))))).....((((.....))))..))))))............ (-27.70 = -27.70 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	11,401,676 – 11,401,796
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.17
Mean single sequence MFE	-26.65
Consensus MFE	-25.28
Energy contribution	-24.88
Covariance contribution	-0.40
Combinations/Pair	1.06
Mean z-score	-2.12
Structure conservation index	0.95
SVM decision value	2.87
SVM RNA-class probability	0.997519
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11401676 120 + 27905053
UCUUCACAUUUUAAUGGCCAUCGCCACAAUCCGUUAAGAGUUGGAAUUUUAUUUCUCGUAAAAGAAAUACAAUUUGAGCAUCAUUAAACGGAAAAUGGUUGCCUGCACCAAUUUCGUUUC
...............(((....((((...(((((((((((((.(((((.(((((((......))))))).))))).))).)).)).))))))...)))).)))................. ( -26.50)
>DroSec_CAF1 149342 120 + 1
UCUUCACAUUUUAAUGGCCAUCGCCACAAUCCGUUAAGAGUUGGAAUUUUAUUUCUCGUAAAAGAAAUACAAUUUGAGCAUCAUUAAACGGAAAAUGGUUGCCUGCACCAAUUUCGUUUC
...............(((....((((...(((((((((((((.(((((.(((((((......))))))).))))).))).)).)).))))))...)))).)))................. ( -26.50)
>DroSim_CAF1 140408 120 + 1
UCUUCACAUUUUAAUGGCCAUCGCCACAAUCCGUUAAGAGUUGGAAUUUUAUUUCUCGUAAAAGAAAUACAAUUUGAGCAUCAUUAAACGGAAAAUGGUUGCCUGCACCAAUUUCGUUUC
...............(((....((((...(((((((((((((.(((((.(((((((......))))))).))))).))).)).)).))))))...)))).)))................. ( -26.50)
>DroEre_CAF1 137423 119 + 1
UCUUCACAUUUUAAUGGCCAUCGCCACAAUCCGUUAAGAGUUGGAGUUUUAUUUCUCGUAAAAGAAAUACAAUUUGAGCAUCAUUAAACGAAA-AGGGUUCCCUGCACCAAUUUCGUUUC
((((.((.......((((....))))......)).))))(((.(((((.(((((((......))))))).))))).)))......((((((((-..(((.......)))..)))))))). ( -26.82)
>DroYak_CAF1 140411 120 + 1
UCUUCACAUUUUAAUGGCCAUCGCCACAAUCCGUUAAGAGUUGGAAUUUUAUUUCUCGUAAAAGAAAUACAAUUUGAGCAUCAUUAAACGAAAAAUGGUUGCCUGCACCAAUUUCGUUUC
((((.((.......((((....))))......)).))))(((.(((((.(((((((......))))))).))))).)))......((((((((..((((.(....))))).)))))))). ( -26.92)
>consensus
UCUUCACAUUUUAAUGGCCAUCGCCACAAUCCGUUAAGAGUUGGAAUUUUAUUUCUCGUAAAAGAAAUACAAUUUGAGCAUCAUUAAACGGAAAAUGGUUGCCUGCACCAAUUUCGUUUC
((((.((.......((((....))))......)).))))(((.(((((.(((((((......))))))).))))).)))......((((((((...(((.......)))..)))))))). (-25.28 = -24.88 +  -0.40)

alignment

secondary structure

dotplot

Window 3

Location	11,401,716 – 11,401,836
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.39
Mean single sequence MFE	-26.38
Consensus MFE	-22.88
Energy contribution	-23.32
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.70
Structure conservation index	0.87
SVM decision value	1.50
SVM RNA-class probability	0.959395
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11401716 120 - 27905053
GGAGUCGUUUUUUUUUUUUAGGUGUUUGAAAAAAUAUUAGGAAACGAAAUUGGUGCAGGCAACCAUUUUCCGUUUAAUGAUGCUCAAAUUGUAUUUCUUUUACGAGAAAUAAAAUUCCAA
(((((((((...........(((((((....)))))))...((((((((.((((.......)))).))).)))))))))))..........((((((((....))))))))....))).. ( -24.70)
>DroSec_CAF1 149382 117 - 1
GGAGUCGGUUU---UUUUUAGGUGUUUGAAAAAAUAUUAGGAAACGAAAUUGGUGCAGGCAACCAUUUUCCGUUUAAUGAUGCUCAAAUUGUAUUUCUUUUACGAGAAAUAAAAUUCCAA
(((((((((((---(((...(((((((....))))))))))))))((((.((((.......)))).)))).......))))..........((((((((....))))))))....))).. ( -24.50)
>DroSim_CAF1 140448 117 - 1
GGAGACGGUUU---UUUUUAGGUGUUUGAAAAAAUAUUAGGAAACGAAAUUGGUGCAGGCAACCAUUUUCCGUUUAAUGAUGCUCAAAUUGUAUUUCUUUUACGAGAAAUAAAAUUCCAA
(((((((((((---(((...(((((((....))))))))))))))((((.((((.......)))).)))))))))...........((((.((((((((....)))))))).)))))).. ( -25.80)
>DroEre_CAF1 137463 114 - 1
GGAGUCAGUUG-----UUCAGGUGUUUGAAAAAAUAUUAAGAAACGAAAUUGGUGCAGGGAACCCU-UUUCGUUUAAUGAUGCUCAAAUUGUAUUUCUUUUACGAGAAAUAAAACUCCAA
(((((.(((..-----.((((((((((....)))))))...((((((((..(((.......)))..-))))))))..))).))).......((((((((....))))))))..))))).. ( -29.40)
>DroYak_CAF1 140451 115 - 1
GGAGUCAGUUG-----UUCAGGUGUUUGAAAAAAUAUUAAGAAACGAAAUUGGUGCAGGCAACCAUUUUUCGUUUAAUGAUGCUCAAAUUGUAUUUCUUUUACGAGAAAUAAAAUUCCAA
(((((.(((..-----.((((((((((....)))))))...((((((((.((((.......))))..))))))))..))).))).......((((((((....))))))))..))))).. ( -27.50)
>consensus
GGAGUCGGUUU___UUUUUAGGUGUUUGAAAAAAUAUUAGGAAACGAAAUUGGUGCAGGCAACCAUUUUCCGUUUAAUGAUGCUCAAAUUGUAUUUCUUUUACGAGAAAUAAAAUUCCAA
(((((..................((((((.....(((((..((((((((.((((.......)))).))).)))))..))))).))))))..((((((((....))))))))..))))).. (-22.88 = -23.32 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:15 2006