Locus 3150

Sequence ID	2L_DroMel_CAF1
Location	8,988,220 – 8,988,384
Length	164
Max. P	0.859776

overview

Window 4

Location	8,988,220 – 8,988,310
Length	90
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	73.80
Mean single sequence MFE	-14.15
Consensus MFE	-8.34
Energy contribution	-7.82
Covariance contribution	-0.52
Combinations/Pair	1.31
Mean z-score	-1.39
Structure conservation index	0.59
SVM decision value	0.19
SVM RNA-class probability	0.626940
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8988220 90 - 22407834
UUAAUUAAUUCGUAUUUAAUUAGCACAGCUAAACUAAAAGCUGGG----CUCUAUUCAA-------------------AGUUGUAUUGCUCUAAACAAAUAUCACGAA-U------AGAA
.(((((((.......)))))))((.(((((........))))).)----)(((((((..-------------------.((.(((((..........))))).)))))-)------))). ( -18.60)
>DroSec_CAF1 32470 90 - 1
UUAAUUAAUUCGUAUUUAAUUAGAACAGCUAAACUAAAAGCUGGG----CUCUAUUCAA-------------------ACAUAUACUGCUCUAAACAAAUAUCACACA-U------AGAA
...........((((((..(((((.(((((........))))).(----(..(((....-------------------....)))..)))))))..))))))......-.------.... ( -12.90)
>DroSim_CAF1 25909 76 - 1
UUAAUUAAUUCGUAUUUAAUUAGCACAGCUAAACUAAAAGCUGU-------------------------------------UGUAUUGCUCUAAACAAAUAUCACACA-U------AGAA
.(((((((.......)))))))((((((((........))))).-------------------------------------)))........................-.------.... ( -10.20)
>DroEre_CAF1 55170 90 - 1
UUAAUUAGUUCGUAUUUAAUUAGCACAGCUAAACUAAAAGCUGGG----CUCUAUACAA-------------------AGUUGUACUGCUCUAGGCAAAUAUCACACA-U------AGAG
.(((((((.......)))))))((.(((((........))))).)----)((((((((.-------------------...)))..(((.....)))..........)-)------))). ( -15.50)
>DroYak_CAF1 51038 90 - 1
UUAAUUAAUUCGUAUUUAAUUAGCACAGCUAAACUAAAAGCUGCG----CUCUAUUCAA-------------------ACUUGUACUGCUCUAAACAAAUAUCACACA-U------AAAA
.(((((((.......)))))))((.(((((........))))).)----).........-------------------..............................-.------.... ( -11.90)
>DroAna_CAF1 66804 120 - 1
CUAAUUAAUUCGAAUUUAAUUAGCGUGGCCCAACUAAAAGCUAAGUAAACACUCUUCACGCUACUCCCAGGUUUUGGCAGCUGUAGGAUUCUAAACAAACAUCAAGAUUUAGUUCAAGAA
..((((((.((...((((.(((((.(((.....)))...))))).))))...((((((.(((....((((...)))).))))).)))).................)).))))))...... ( -15.80)
>consensus
UUAAUUAAUUCGUAUUUAAUUAGCACAGCUAAACUAAAAGCUGGG____CUCUAUUCAA___________________AGUUGUACUGCUCUAAACAAAUAUCACACA_U______AGAA
((((((((.......))))))))..(((((........)))))............................................................................. ( -8.34 =  -7.82 +  -0.52)

alignment

secondary structure

dotplot

Window 5

Location	8,988,253 – 8,988,345
Length	92
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.45
Mean single sequence MFE	-19.93
Consensus MFE	-13.85
Energy contribution	-12.97
Covariance contribution	-0.88
Combinations/Pair	1.47
Mean z-score	-1.30
Structure conservation index	0.69
SVM decision value	0.63
SVM RNA-class probability	0.805322
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8988253 92 - 22407834
GUUAUGGUGAGAACAC-AUUGUACAC----GCAGGCAUUGUUAAUUAAUUCGUAUUUAAUUAGCACAGCUAAACUAAAAGCUGGG----CUCUAUUCAA-------------------AG
((((..(((......)-))..)).))----..((((..((((((((((.......))))))))))(((((........))))).)----).))......-------------------.. ( -20.00)
>DroSec_CAF1 32503 92 - 1
GUUAUGGUGAGAACAC-ACUGUACAC----GCAGGCAUUGUUAAUUAAUUCGUAUUUAAUUAGAACAGCUAAACUAAAAGCUGGG----CUCUAUUCAA-------------------AC
(((((((((......)-)))))).))----..((((....((((((((.......))))))))..(((((........))))).)----).))......-------------------.. ( -17.20)
>DroSim_CAF1 25941 79 - 1
GUUAUGGUGAGAACAC-ACUGUACAC----GCAGGCAUUGUUAAUUAAUUCGUAUUUAAUUAGCACAGCUAAACUAAAAGCUGU------------------------------------
(((((((((......)-)))))).))----.........(((((((((.......)))))))))((((((........))))))------------------------------------ ( -18.50)
>DroEre_CAF1 55203 92 - 1
GUUAUGGUGAGAAUAA-ACUGUACAC----GCAGGCAUUGUUAAUUAGUUCGUAUUUAAUUAGCACAGCUAAACUAAAAGCUGGG----CUCUAUACAA-------------------AG
......((((((....-.((((....----))))((..((((((((((.......))))))))))(((((........))))).)----)))).)))..-------------------.. ( -20.70)
>DroYak_CAF1 51071 96 - 1
GUUAUGGUGAGAACUC-ACUACACACGCACGCAGGCAUUGUUAAUUAAUUCGUAUUUAAUUAGCACAGCUAAACUAAAAGCUGCG----CUCUAUUCAA-------------------AC
....((((((....))-))))...........((((..((((((((((.......))))))))))(((((........))))).)----).))......-------------------.. ( -21.10)
>DroAna_CAF1 66844 116 - 1
UUUAUGGUGAGAAAAAAAGAGCACAC----GUAUGCAAUGCUAAUUAAUUCGAAUUUAAUUAGCGUGGCCCAACUAAAAGCUAAGUAAACACUCUUCACGCUACUCCCAGGUUUUGGCAG
....(((.(((.....(((((.....----....((.(((((((((((.......))))))))))).))...(((........))).....))))).......))))))........... ( -22.10)
>consensus
GUUAUGGUGAGAACAC_ACUGUACAC____GCAGGCAUUGUUAAUUAAUUCGUAUUUAAUUAGCACAGCUAAACUAAAAGCUGGG____CUCUAUUCAA___________________AG
..................((((........))))....((((((((((.......))))))))))(((((........)))))..................................... (-13.85 = -12.97 +  -0.88)

alignment

secondary structure

dotplot

Window 6

Location	8,988,270 – 8,988,384
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.05
Mean single sequence MFE	-21.90
Consensus MFE	-14.08
Energy contribution	-14.00
Covariance contribution	-0.08
Combinations/Pair	1.36
Mean z-score	-2.34
Structure conservation index	0.64
SVM decision value	0.82
SVM RNA-class probability	0.859776
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8988270 114 - 22407834
ACAAAAAAAAAAAAGC-GAAGUUCACAGAGAACAUAAAAUGUUAUGGUGAGAACAC-AUUGUACAC----GCAGGCAUUGUUAAUUAAUUCGUAUUUAAUUAGCACAGCUAAACUAAAAG
..............((-(..((((.....))))......(((.(..(((......)-))..)))))----)).(((..((((((((((.......))))))))))..))).......... ( -22.30)
>DroSec_CAF1 32520 114 - 1
ACAACAAAAAAAAAGC-GAAGUUCACAGAGAACAUAAAAUGUUAUGGUGAGAACAC-ACUGUACAC----GCAGGCAUUGUUAAUUAAUUCGUAUUUAAUUAGAACAGCUAAACUAAAAG
..............((-(..((((.....))))......(((.((((((......)-)))))))))----)).(((....((((((((.......))))))))....))).......... ( -19.60)
>DroSim_CAF1 25945 110 - 1
ACA----AAAAAAAGC-GAAGUUCACAGAGAACAUAAAAUGUUAUGGUGAGAACAC-ACUGUACAC----GCAGGCAUUGUUAAUUAAUUCGUAUUUAAUUAGCACAGCUAAACUAAAAG
...----.......((-(..((((.....))))......(((.((((((......)-)))))))))----)).(((..((((((((((.......))))))))))..))).......... ( -23.80)
>DroEre_CAF1 55220 108 - 1
ACAA-------AAAGGGGCAGUUCACAGAGAACAUAAAAUGUUAUGGUGAGAAUAA-ACUGUACAC----GCAGGCAUUGUUAAUUAGUUCGUAUUUAAUUAGCACAGCUAAACUAAAAG
....-------....(..((((((((....(((((...)))))...))))......-))))..)..----...(((..((((((((((.......))))))))))..))).......... ( -20.40)
>DroYak_CAF1 51088 111 - 1
ACCA-------AAAGC-GAAGUUCACAGAGAACAUAAAAUGUUAUGGUGAGAACUC-ACUACACACGCACGCAGGCAUUGUUAAUUAAUUCGUAUUUAAUUAGCACAGCUAAACUAAAAG
....-------...((-(..((((.....))))......(((..((((((....))-)))).)))))).....(((..((((((((((.......))))))))))..))).......... ( -24.50)
>DroAna_CAF1 66884 94 - 1
ACAU-------A---C-AAAGUUUUU-----------AGUUUUAUGGUGAGAAAAAAAGAGCACAC----GUAUGCAAUGCUAAUUAAUUCGAAUUUAAUUAGCGUGGCCCAACUAAAAG
....-------.---.-.....((((-----------((((.(((((((............))).)----))).((.(((((((((((.......))))))))))).))..)))))))). ( -20.80)
>consensus
ACAA_______AAAGC_GAAGUUCACAGAGAACAUAAAAUGUUAUGGUGAGAACAC_ACUGUACAC____GCAGGCAUUGUUAAUUAAUUCGUAUUUAAUUAGCACAGCUAAACUAAAAG
.....................(((((....((((.....))))...))))).......((((........))))((..((((((((((.......))))))))))..))........... (-14.08 = -14.00 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:31 2006