Locus 4760

Sequence ID	2L_DroMel_CAF1
Location	13,575,435 – 13,575,708
Length	273
Max. P	0.941484

overview

Window 2

Location	13,575,435 – 13,575,551
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.43
Mean single sequence MFE	-33.73
Consensus MFE	-29.77
Energy contribution	-30.77
Covariance contribution	1.00
Combinations/Pair	1.12
Mean z-score	-2.02
Structure conservation index	0.88
SVM decision value	1.32
SVM RNA-class probability	0.941484
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13575435 116 + 22407834
----CAAUGACAUUUUUGAAGCAAACUCCUUUAGAUUAUCUAUUGCAUUCAUCCAGAUAACUUCGGGCGCACAGUGCAUCGGGGAAAAUGGUUGCACUGGGAUGGUUGCAGUGGACUUCC
----..........(((((((.......)))))))...(((((((((..(((((......(....).....((((((((((.......))).))))))))))))..)))))))))..... ( -35.90)
>DroSec_CAF1 8604 116 + 1
----CAAUGACAUUUUUAAAGCAAACUCCUUUAGAUUAUCUAUUGCAUUCAUCCAGAUAACUACGAGCGCACAGUGCAUCGUGGAAAAUGGUUGCACUGGGAUGGUUGCAGUGGACUUCC
----..........(((((((.......)))))))...(((((((((..(((((((....)).........(((((((((((.....)))).))))))))))))..)))))))))..... ( -35.10)
>DroSim_CAF1 8380 116 + 1
----AAAUGACAUUUUUGAAGCAAACUCCUUUAGAUUAUCUAUUGCAUUCAUCCAGAUAACUACGAGCGCACAGUGCAUCGUGGAAAAUGGUUGCACUGGGAUGGUUGCAGUGGACUUCC
----..........(((((((.......)))))))...(((((((((..(((((((....)).........(((((((((((.....)))).))))))))))))..)))))))))..... ( -35.20)
>DroEre_CAF1 9086 117 + 1
UUUACAAUCACAUCUUCGAAACAAACUCCUUUAGAUAAUCUAUGGUAUGCAUCUUGAUGACUUUGGGAACACAGUGCACCGUUGAAAAUGGUUGCACUGGGAU---GGCAGUGGACUUCC
....((....(((((...........((((..((...(((...(((....)))..)))..))..))))...(((((((((((.....)))).)))))))))))---)....))....... ( -28.70)
>consensus
____CAAUGACAUUUUUGAAGCAAACUCCUUUAGAUUAUCUAUUGCAUUCAUCCAGAUAACUACGAGCGCACAGUGCAUCGUGGAAAAUGGUUGCACUGGGAUGGUUGCAGUGGACUUCC
..............(((((((.......)))))))...(((((((((.((((((..........(....).(((((((((((.....)))).))))))))))))).)))))))))..... (-29.77 = -30.77 +   1.00)

alignment

secondary structure

dotplot

Window 3

Location	13,575,471 – 13,575,591
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.92
Mean single sequence MFE	-35.62
Consensus MFE	-28.80
Energy contribution	-29.16
Covariance contribution	0.36
Combinations/Pair	1.15
Mean z-score	-1.39
Structure conservation index	0.81
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13575471 120 + 22407834
UAUUGCAUUCAUCCAGAUAACUUCGGGCGCACAGUGCAUCGGGGAAAAUGGUUGCACUGGGAUGGUUGCAGUGGACUUCCGUUAUGGUCAUAGCAACCUGCUCAACAUGUUAAUGCAACG
..((((((((((...((.....))((((...((((((((((.......))).)))))))....((((((.(((.(((........)))))).)))))).))))...)))..))))))).. ( -36.80)
>DroSec_CAF1 8640 120 + 1
UAUUGCAUUCAUCCAGAUAACUACGAGCGCACAGUGCAUCGUGGAAAAUGGUUGCACUGGGAUGGUUGCAGUGGACUUCCGUUAUGGUCAUAGCAACCUGCUCAACAUGUUAAUGCAACG
..((((((((.....))((((...((((...(((((((((((.....)))).)))))))....((((((.(((.(((........)))))).)))))).)))).....)))))))))).. ( -38.30)
>DroSim_CAF1 8416 120 + 1
UAUUGCAUUCAUCCAGAUAACUACGAGCGCACAGUGCAUCGUGGAAAAUGGUUGCACUGGGAUGGUUGCAGUGGACUUCCGUUAUGGUCAUAGCAACCUGCUCAACAUGUUAAUGCAACG
..((((((((.....))((((...((((...(((((((((((.....)))).)))))))....((((((.(((.(((........)))))).)))))).)))).....)))))))))).. ( -38.30)
>DroEre_CAF1 9126 117 + 1
UAUGGUAUGCAUCUUGAUGACUUUGGGAACACAGUGCACCGUUGAAAAUGGUUGCACUGGGAU---GGCAGUGGACUUCCGUUAUGGUCAUAGCAACCUGCUCAACAUGUUAUUGCAACG
....(((.((((.(((((((((.((....))(((((((((((.....)))).))))))).(((---((.((....)).)))))..))))))(((.....)))))).))))...))).... ( -33.80)
>DroYak_CAF1 5774 105 + 1
---------------GAUAACUUUGGGAACACAGUGCAUCGUUGAAAAUGGUUGCACUGGGAUGGUGGCAGUGGACUUCCGUUAUGGUCAUAGCAACCUGCUCAACAUGUUAAUGCAACG
---------------(((.(((.((....)).)))..)))..........((((((.(((.(((.((((((.((....))(((((....)))))...)))).)).))).))).)))))). ( -30.90)
>consensus
UAUUGCAUUCAUCCAGAUAACUUCGGGCGCACAGUGCAUCGUGGAAAAUGGUUGCACUGGGAUGGUUGCAGUGGACUUCCGUUAUGGUCAUAGCAACCUGCUCAACAUGUUAAUGCAACG
....................((((((((((...)))).))))))......((((((.(((.(((...((((.((....))(((((....)))))...))))....))).))).)))))). (-28.80 = -29.16 +   0.36)

alignment

secondary structure

dotplot

Window 4

Location	13,575,591 – 13,575,708
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.52
Mean single sequence MFE	-30.34
Consensus MFE	-24.42
Energy contribution	-25.34
Covariance contribution	0.92
Combinations/Pair	1.07
Mean z-score	-1.82
Structure conservation index	0.80
SVM decision value	0.89
SVM RNA-class probability	0.875806
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13575591 117 - 22407834
C---ACACCCAACCGCACCCUACCCGAUUCCAACUAACCCCCAAACCAGUUGCCACCGACCCAAUCUCUGUGGGGCUGUUGUCAAGCAGCAGCUGCAUGGGAAUUUGGAUUUUGGUUCGC
.---..........((.....(((.((.(((((......((((...(((((((......((((.......))))(((.......))).)))))))..))))...))))).)).)))..)) ( -31.10)
>DroSec_CAF1 8760 116 - 1
CUCCACACCC---CACACCCUACACCAUUCCAACUAAACCCCA-ACCAGUUGCCACCGACCCAAUCCCUGUGGGGCUGUUGUCAAGCAGCAGCUGCAUGGGAAUUUGGAUUUUGGUUCGC
..........---..........((((.(((((..........-....((((....))))....((((.(((.((((((((.....)))))))).)))))))..)))))...)))).... ( -33.30)
>DroSim_CAF1 8536 114 - 1
CUCCACACCC---C--ACCCUACCCCAUUCCAACUAAACCCCA-ACCAGUUGCCACCGACCCAAUCCCUGUGGGGCUGUUGUCAAGCAGCAGCUGCAUGGGAAUUUGGAUUUUGGUUCGC
..........---.--...............(((((((..(((-(...((((....))))....((((.(((.((((((((.....)))))))).)))))))..))))..)))))))... ( -32.50)
>DroEre_CAF1 9243 94 - 1
------------------------CCAUUCCACCUAACCCCCA-ACCAGA-UCCACCGACCCAAUCUCCGUGGGGUUGUUGUCAAGCAGCUGCUGCAUGGGAAUUUGGAUUUUGGUUCGC
------------------------..................(-((((((-((((.......(((..(((((.(((.((((.....)))).))).)))))..))))))).)))))))... ( -27.41)
>DroYak_CAF1 5879 93 - 1
------------------------CCAUUCCACCCAACCCCCA-ACCAGAACCCAACGCCCCAAUCUCUGUGGGGUUGUUGUCAAGCAGCUGCUGC--GGGAAUUUGGAUUUUGGUUCGC
------------------------(((.(((((((........-.........((((((((((.......))))).)))))....((((...))))--)))....))))...)))..... ( -27.40)
>consensus
C___ACACCC___C__ACCCUAC_CCAUUCCAACUAACCCCCA_ACCAGUUGCCACCGACCCAAUCUCUGUGGGGCUGUUGUCAAGCAGCAGCUGCAUGGGAAUUUGGAUUUUGGUUCGC
........................(((.(((((......((((...(((((........((((.......))))((((((....)))))))))))..))))...)))))...)))..... (-24.42 = -25.34 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:37 2006