Locus 8721

Sequence ID	3R_DroMel_CAF1
Location	23,303,005 – 23,303,144
Length	139
Max. P	0.997184

overview

Window 4

Location	23,303,005 – 23,303,115
Length	110
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	78.91
Mean single sequence MFE	-27.52
Consensus MFE	-18.88
Energy contribution	-19.28
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.11
Structure conservation index	0.69
SVM decision value	1.38
SVM RNA-class probability	0.947969
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23303005 110 + 27905053
CUGUUUUUUUUUUAUAUAAA-----ACAGCAAGUU----CUGCAGGGUAUCAAAACUGCUUUGUCGCAAAGCAUACUUUUGCAUGUGCCAAAGCAAUUGUACAGUGCUCGCCCAGCAAA
(((((((..........)))-----))))...(((----..((.((((((...((.(((((((.((((..(((......))).)))).))))))).)).....))))))))..)))... ( -27.90)
>DroSec_CAF1 100414 105 + 1
----UUUUGUUUGAUAUGGA-----ACAGCAAGUU----CUGCAGGGUAUCAAAACUGCUUU-UAGCAAAGCAUGCUUUUGCAUGUGCCAAAGCAAUUGUACAGUGCUUUCCCAGCAAA
----.((((((.(....(((-----((.....)))----))(((..(((.(((...((((((-..((...((((((....)))))))).)))))).))))))..)))....).)))))) ( -26.90)
>DroSim_CAF1 104284 83 + 1
----UUU---------------------------U----CUGCAGGGUAUCAAAACUGCUUU-UCGCAAAGCAUGCUUUUGCAUGUGCCAAAGCAAUUGUACAGUGCUUUCCCAGCAAA
----...---------------------------.----..(((..(((.(((...((((((-..((...((((((....)))))))).)))))).))))))..)))............ ( -21.20)
>DroEre_CAF1 106862 108 + 1
----CU----UCGAUAUAAAAAU--ACAGCAAGUUGGUGCUGCAGGGUAUCAAAACUGCUUU-UCGCAAAGCAUGCUGUGGCCUGUGCCAAAGCAAUUGUACAGUGCUUUCCCAGCAAA
----..----..(((((......--.(((((......)))))....))))).....((((((-....))))))(((((.(((((((((..((....)))))))).)))....))))).. ( -29.70)
>DroYak_CAF1 110803 114 + 1
----CUUUGUUUAAUAGAAAAAUAAACAGUAAGUUAUUUCAGCAGGGUAUCAAAGCUGCUUU-UCGCAAAGCAUGCUUUGGCAUGUGCCAAAGCAAUUGUACAGUGCUUUCCCAGCAAA
----..(((((((.........)))))))............((.(((....(((((((((((-....))))))(((((((((....)))))))))..........)))))))).))... ( -31.90)
>consensus
____UUUU_UUUGAUAUAAA_____ACAGCAAGUU____CUGCAGGGUAUCAAAACUGCUUU_UCGCAAAGCAUGCUUUUGCAUGUGCCAAAGCAAUUGUACAGUGCUUUCCCAGCAAA
.........................................(((..(((.(((...((((((...((...((((((....)))))))).)))))).))))))..)))............ (-18.88 = -19.28 +   0.40)

alignment

secondary structure

dotplot

Window 5

Location	23,303,005 – 23,303,115
Length	110
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	78.91
Mean single sequence MFE	-30.22
Consensus MFE	-22.08
Energy contribution	-22.20
Covariance contribution	0.12
Combinations/Pair	1.12
Mean z-score	-2.84
Structure conservation index	0.73
SVM decision value	2.81
SVM RNA-class probability	0.997184
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23303005 110 - 27905053
UUUGCUGGGCGAGCACUGUACAAUUGCUUUGGCACAUGCAAAAGUAUGCUUUGCGACAAAGCAGUUUUGAUACCCUGCAG----AACUUGCUGU-----UUUAUAUAAAAAAAAAACAG
(((((.(((.......(((..((((((((((((((((((....)))))...)))..))))))))))...)))))).))))----).....((((-----(((..........))))))) ( -27.91)
>DroSec_CAF1 100414 105 - 1
UUUGCUGGGAAAGCACUGUACAAUUGCUUUGGCACAUGCAAAAGCAUGCUUUGCUA-AAAGCAGUUUUGAUACCCUGCAG----AACUUGCUGU-----UCCAUAUCAAACAAAA----
((((.(((((.((((.........(((((((((((((((....)))))...)))).-))))))((((((........)))----))).)))).)-----))))...)))).....---- ( -30.00)
>DroSim_CAF1 104284 83 - 1
UUUGCUGGGAAAGCACUGUACAAUUGCUUUGGCACAUGCAAAAGCAUGCUUUGCGA-AAAGCAGUUUUGAUACCCUGCAG----A---------------------------AAA----
(((((.((((((((..........((((((.((....)).))))))((((((....-)))))))))))....))).))))----)---------------------------...---- ( -26.00)
>DroEre_CAF1 106862 108 - 1
UUUGCUGGGAAAGCACUGUACAAUUGCUUUGGCACAGGCCACAGCAUGCUUUGCGA-AAAGCAGUUUUGAUACCCUGCAGCACCAACUUGCUGU--AUUUUUAUAUCGA----AG----
..(((((..((((((.(.....).))))))(((....))).)))))((((((....-))))))..(((((((...(((((((......))))))--)......))))))----).---- ( -32.90)
>DroYak_CAF1 110803 114 - 1
UUUGCUGGGAAAGCACUGUACAAUUGCUUUGGCACAUGCCAAAGCAUGCUUUGCGA-AAAGCAGCUUUGAUACCCUGCUGAAAUAACUUACUGUUUAUUUUUCUAUUAAACAAAG----
...((.((((((((..........(((((((((....)))))))))((((((....-)))))))))))....))).)).............((((((.........))))))...---- ( -34.30)
>consensus
UUUGCUGGGAAAGCACUGUACAAUUGCUUUGGCACAUGCAAAAGCAUGCUUUGCGA_AAAGCAGUUUUGAUACCCUGCAG____AACUUGCUGU_____UUUAUAUCAAA_AAAA____
.((((.((((((((..........((((((.((....)).))))))((((((.....)))))))))))....))).))))....................................... (-22.08 = -22.20 +   0.12)

alignment

secondary structure

dotplot

Window 6

Location	23,303,036 – 23,303,144
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.81
Mean single sequence MFE	-37.02
Consensus MFE	-18.85
Energy contribution	-21.53
Covariance contribution	2.68
Combinations/Pair	1.03
Mean z-score	-3.75
Structure conservation index	0.51
SVM decision value	0.86
SVM RNA-class probability	0.868495
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23303036 108 - 27905053
CUUCCAGUUUGGCGGUAAAUCAUCAC-----------CGUUUUGCUGGGCGA-GCACUGUACAAUUGCUUUGGCACAUGCAAAAGUAUGCUUUGCGACAAAGCAGUUUUGAUACCCUGCA
..((((((..((((((........))-----------))))..))))))...-(((..((((((((((((((((((((((....)))))...)))..)))))))))..)).)))..))). ( -37.10)
>DroSec_CAF1 100441 107 - 1
CUUCCAGUUUGGCGGUAAAUCAUCAC-----------CGUUUUGCUGGGAAA-GCACUGUACAAUUGCUUUGGCACAUGCAAAAGCAUGCUUUGCUA-AAAGCAGUUUUGAUACCCUGCA
.(((((((..((((((........))-----------))))..)))))))..-(((..((((((((((((((((((((((....)))))...)))).-))))))))..)).)))..))). ( -40.60)
>DroSim_CAF1 104289 107 - 1
CUUCCAGUUUGGCGGUAAAUCAUCAC-----------CGUUUUGCUGGGAAA-GCACUGUACAAUUGCUUUGGCACAUGCAAAAGCAUGCUUUGCGA-AAAGCAGUUUUGAUACCCUGCA
.(((((((..((((((........))-----------))))..)))))))..-(((..(((((((((((((.((((((((....)))))...)))..-))))))))..)).)))..))). ( -39.70)
>DroEre_CAF1 106892 107 - 1
CUUCCAGUUUGGCGGUAAAUCAUCGC-----------CGUUUUGCUGGGAAA-GCACUGUACAAUUGCUUUGGCACAGGCCACAGCAUGCUUUGCGA-AAAGCAGUUUUGAUACCCUGCA
.(((((((.(((((((.....)))))-----------))....)))))))..-(((..((((((.((((.((((....)))).))))((((((....-))))))...))).)))..))). ( -40.80)
>DroYak_CAF1 110839 107 - 1
CUUCCAGUUUGGCGGUAAAUCAUCAC-----------CGUUUUGCUGGGAAA-GCACUGUACAAUUGCUUUGGCACAUGCCAAAGCAUGCUUUGCGA-AAAGCAGCUUUGAUACCCUGCU
.(((((((..((((((........))-----------))))..))))))).(-(((..((((((.(((((((((....)))))))))((((((....-))))))...))).)))..)))) ( -44.40)
>DroAna_CAF1 97417 102 - 1
CUUGCAUUUUGGCGGUAAAUCAUCGCACACAGCCACACAAUUUGCUCAGAAAUGCACACUACAAUUGCGU----AAAU------GCAUCACCU-------ACCAGUUUUG-UAUCCUGGA
..((((((((((((((.....))))).)).....((.((((((((........)))......))))).))----))))------)))......-------.((((.....-....)))). ( -19.50)
>consensus
CUUCCAGUUUGGCGGUAAAUCAUCAC___________CGUUUUGCUGGGAAA_GCACUGUACAAUUGCUUUGGCACAUGCAAAAGCAUGCUUUGCGA_AAAGCAGUUUUGAUACCCUGCA
.(((((((..((((.......................))))..)))))))...(((..(((((((((((((.((((((((....)))))...)))...))))))))..)).)))..))). (-18.85 = -21.53 +   2.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:18:05 2006