Locus 3918

Sequence ID	2R_DroMel_CAF1
Location	12,907,082 – 12,907,213
Length	131
Max. P	0.694534

overview

Window 7

Location	12,907,082 – 12,907,188
Length	106
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	80.51
Mean single sequence MFE	-24.93
Consensus MFE	-20.72
Energy contribution	-20.58
Covariance contribution	-0.14
Combinations/Pair	1.06
Mean z-score	-1.32
Structure conservation index	0.83
SVM decision value	0.34
SVM RNA-class probability	0.694534
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12907082 106 - 20766785
-CAU--AAAACACGAAAAAAAUGAA--A--------AGCAAAAAAUUGUACUUGGAGAUGCCGGGGAUUGAACCCGGGGCCUCUCACAUGCAAAGCGAGCGCUCUACCACUGAGCUACA
-...--...................--.--------.((......(((((..(((((.(.(((((.......))))).).))).))..))))).....))((((.......)))).... ( -26.10)
>DroPse_CAF1 28580 103 - 1
-CAU--UAAA----AUAGAGAAUAAAGA--------GACAAAAAA-UGUACUUGGAGAUGCCGGGGAUUGAACCCGGGGCCUCUCACAUGCAAAGCGAGCGCUCUACCACUGAGCUACA
-...--....----..............--------.........-((((..(((((.(.(((((.......))))).).))).))..))))........((((.......)))).... ( -24.30)
>DroGri_CAF1 26595 103 - 1
UUUUUGAAAA-----AUACCGAAAA--A--------AACAAAAAG-UUGAAUUGGAGAUGCCGGGGAUUGAACCCGGGGCCUCUCACAUGCAAAGCGAGCGCUCUACCACUGAGCUACA
((((((....-----....))))))--.--------........(-((....(((((((.(((((.......))))).)..)))).)).....)))....((((.......)))).... ( -24.10)
>DroWil_CAF1 51685 109 - 1
------AAAGAGUAAGAAAAAAGAA--AUUGGCAUUAAAAAAAAU-UGUAC-UGGAGAUGCCGGGGAUUGAACCCGGGGCCUCUCACAUGCAAAGCGAGCGCUCUACCACUGAGCUACA
------.....(((...........--.................(-((((.-(((((((.(((((.......))))).)..)))).))))))).......((((.......))))))). ( -25.60)
>DroAna_CAF1 30468 98 - 1
-------AAAA---UAAAUAAAAUA--A--------GGCAAAAAA-UGUACUUGGAGAUGCCGGGGAUUGAACCCGGGGCCUCUCACAUGCAAAGCGAGCGCUCUACCACUGAGCUACA
-------....---...........--.--------.((......-((((..(((((.(.(((((.......))))).).))).))..))))......))((((.......)))).... ( -25.40)
>DroPer_CAF1 17188 96 - 1
-C-----AGA----AAAGAGAAGAA--A--------AUCAAAAUA-UGU-CUUGGAGAUGCCGGGGAUUGAACCUG-GGCCUCUCACAUGCAAAGCGAGCGCUCUACCAAUGAGCUACA
-.-----...----...........--.--------.........-(((-..((((((.(((.(((......))).-))).)))).)).)))........((((.......)))).... ( -24.10)
>consensus
_C____AAAA____AAAAAAAAGAA__A________AACAAAAAA_UGUACUUGGAGAUGCCGGGGAUUGAACCCGGGGCCUCUCACAUGCAAAGCGAGCGCUCUACCACUGAGCUACA
....................................................((((((.((((((.......)))..))).)))).)).((.......))((((.......)))).... (-20.72 = -20.58 +  -0.14)

alignment

secondary structure

dotplot

Window 8

Location	12,907,122 – 12,907,213
Length	91
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	71.25
Mean single sequence MFE	-13.21
Consensus MFE	-8.10
Energy contribution	-8.10
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.22
Structure conservation index	0.61
SVM decision value	0.20
SVM RNA-class probability	0.631317
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12907122 91 + 20766785
CCCCGGGUUCAAUCCCCGGCAUCUCCAAGUACAAUUUUUUGCUUUUCAUUUUUUUCGUGUUUUAUG---UACUUCCAUAUA--AGCACCGAUCGCG-------
...((((.......))))(((((...(((((........)))))............((((((((((---......)))).)--))))).))).)).------- ( -17.10)
>DroVir_CAF1 28727 93 + 1
CCCCGGGUUCAAUCCCCGGCAUCUCCAAGUACA-UUUUUUGUUAUUUUUCCCUU-----UUUUAAAAUGCACAACCAUUCA--AA--AUACUUUUUCAGUAGA
..(((((.......))))).........((.((-((((................-----....)))))).)).........--..--.((((.....)))).. ( -11.25)
>DroSec_CAF1 30447 91 + 1
CCCCGGGUUCAAUCCCCGGCAUCUCCAAGUACAGUUUUUUGUUUUUCAUUUUUUUCGUGUUUUAUU---UACUUCCAUAUA--AGCACCGAUCGCG-------
...((((.......))))(((((.......((((....))))..............(((((((((.---.......))).)--))))).))).)).------- ( -13.10)
>DroEre_CAF1 32520 87 + 1
CCCCGGGUUCAAUCCCCGGCAUCUCCAAGUACA-UUUUUUGCUUUUCUUUUUUUA---UUUUUAUU---CACAGCGAUCGCUGUG--UUGAUUGCC-------
....(((......))).((((((...(((((..-.....)))))...........---........---((((((....))))))--..)).))))------- ( -18.90)
>DroYak_CAF1 32696 89 + 1
CCCCGGGUUCAAUCCCCGGCAUCUCCAAGUACA-UUUUUUGUUUUCCAUUUUUUG---UUUUUAUU---CACAACCAUAUAUGAGCACCGAUCGUU-------
..(((((.......)))))..............-.....(((((........(((---(.......---.))))........))))).........------- ( -10.79)
>DroAna_CAF1 30508 72 + 1
CCCCGGGUUCAAUCCCCGGCAUCUCCAAGUACA-UUUUUUGCCUUAUUUUAUUUA---UUUU---------UUUCCA---------ACAGAUCG---------
....(((......))).((((............-.....))))............---....---------......---------........--------- (  -8.13)
>consensus
CCCCGGGUUCAAUCCCCGGCAUCUCCAAGUACA_UUUUUUGCUUUUCAUUUUUUA___UUUUUAUU___CACAUCCAUAUA__AG_ACCGAUCGCG_______
..(((((.......))))).................................................................................... ( -8.10 =  -8.10 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	12,907,122 – 12,907,213
Length	91
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	71.25
Mean single sequence MFE	-17.02
Consensus MFE	-10.30
Energy contribution	-10.30
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.29
Structure conservation index	0.60
SVM decision value	0.30
SVM RNA-class probability	0.677520
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12907122 91 - 20766785
-------CGCGAUCGGUGCU--UAUAUGGAAGUA---CAUAAAACACGAAAAAAAUGAAAAGCAAAAAAUUGUACUUGGAGAUGCCGGGGAUUGAACCCGGGG
-------.(((((...((((--(.((((......---))))...((.........))..)))))....)))))...........(((((.......))))).. ( -18.00)
>DroVir_CAF1 28727 93 - 1
UCUACUGAAAAAGUAU--UU--UGAAUGGUUGUGCAUUUUAAAA-----AAGGGAAAAAUAACAAAAAA-UGUACUUGGAGAUGCCGGGGAUUGAACCCGGGG
..((((.....)))).--..--.........(((((((((....-----................))))-))))).........(((((.......))))).. ( -17.95)
>DroSec_CAF1 30447 91 - 1
-------CGCGAUCGGUGCU--UAUAUGGAAGUA---AAUAAAACACGAAAAAAAUGAAAAACAAAAAACUGUACUUGGAGAUGCCGGGGAUUGAACCCGGGG
-------....(((..((((--(......)))))---........................(((......))).......))).(((((.......))))).. ( -13.80)
>DroEre_CAF1 32520 87 - 1
-------GGCAAUCAA--CACAGCGAUCGCUGUG---AAUAAAAA---UAAAAAAAGAAAAGCAAAAAA-UGUACUUGGAGAUGCCGGGGAUUGAACCCGGGG
-------((((.((..--((((((....))))))---........---.............(((.....-))).......))))))(((.......))).... ( -22.30)
>DroYak_CAF1 32696 89 - 1
-------AACGAUCGGUGCUCAUAUAUGGUUGUG---AAUAAAAA---CAAAAAAUGGAAAACAAAAAA-UGUACUUGGAGAUGCCGGGGAUUGAACCCGGGG
-------..(..(.((((((((((......))))---).......---.......((.....)).....-.))))).)..)...(((((.......))))).. ( -17.30)
>DroAna_CAF1 30508 72 - 1
---------CGAUCUGU---------UGGAAA---------AAAA---UAAAUAAAAUAAGGCAAAAAA-UGUACUUGGAGAUGCCGGGGAUUGAACCCGGGG
---------..((((.(---------(....)---------)...---.........(((((((.....-))).)))).)))).(((((.......))))).. ( -12.80)
>consensus
_______AGCGAUCGGU_CU__UAUAUGGAAGUG___AAUAAAAA___AAAAAAAAGAAAAACAAAAAA_UGUACUUGGAGAUGCCGGGGAUUGAACCCGGGG
....................................................................................(((((.......))))).. (-10.30 = -10.30 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:19 2006