Locus 6512

Sequence ID	2R_DroMel_CAF1
Location	20,353,476 – 20,353,577
Length	101
Max. P	0.789600

overview

Window 9

Location	20,353,476 – 20,353,577
Length	101
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	76.43
Mean single sequence MFE	-33.92
Consensus MFE	-13.30
Energy contribution	-14.22
Covariance contribution	0.92
Combinations/Pair	1.29
Mean z-score	-2.16
Structure conservation index	0.39
SVM decision value	0.07
SVM RNA-class probability	0.568217
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20353476 101 + 20766785
UUUGCUGAC-GGAAUGCCAUGUUAGAUGGCAGCAAA---CAUGCCGUUCGAUGGCAAGAGUCG-GGCCAGGCCG-ACUUAAUUGCAUAUUUGCAUAGGCG-CA------GAGC-A
(((((....-....((((((....(((((((.....---..)))))))..)))))).((((((-(......)))-))))...((((....)))).....)-))------))..-. ( -34.10)
>DroPse_CAF1 82553 102 + 1
UUUGCUGAU-GGAAUGCCAUGUUAGAUGACGGCAAA---CAUGCCGCUCCAUGGCAAGAGUCGGGGCCAGGCUG-ACUUAAUUGCAUAUUUGCAUAGGCG-CA------CAGC-A
..(((((((-(.(((((((((...((.(.(((((..---..))))))))))))))..(((((((.......)))-)))).))).)))...(((......)-))------))))-) ( -35.10)
>DroWil_CAF1 134481 105 + 1
ACUGUUGACUGGAAUGCCAUGUUAGAUGGCAACAAACAACAUGCCGCUCAGGCUCAAACUCCG-GCUCAGGCCAAAGUUAAUUGCAUAUUUGCAUAGGCAAGA------GAG---
..(((((..((...((((((.....)))))).))..)))))((((((....))...((((..(-((....)))..))))...((((....))))..))))...------...--- ( -29.90)
>DroMoj_CAF1 110049 90 + 1
UC---AGCU-GGAAUGUCAUGUUAGAUGGCAACAAA---CAUGACGCUCCAUGGCAAAAAGCU-GACCAG-------CUAAUUGCAUAUUUGCAUAGCCA-GC------C---GA
((---.(((-(((.(((((((((...((....))))---))))))).))))((((....((((-....))-------))...((((....))))..))))-))------.---)) ( -33.40)
>DroAna_CAF1 69203 108 + 1
CUUGCUGAC-GGAAUGCCAUGUUAGAUGGCAGCAAA---CACGCUGCUCGAUGGCAAGAGCCGGGGCCCGGCCG-ACUUAAUUGCAUAUUUGCAUAGGCG-CACCAGAAAAGC-A
..((((...-((..((((.(((((...((((((...---...))))))...))))).(.(((((...)))))).-.......((((....))))..))))-..)).....)))-) ( -35.90)
>DroPer_CAF1 82610 102 + 1
UUUGCUGAU-GGAAUGCCAUGUUAGAUGACGGCAAA---CAUGCCGCUCCAUGGCAAGAGUCGGGGCCAGGCUG-ACUUAAUUGCAUAUUUGCAUAGGCG-CA------CAGC-A
..(((((((-(.(((((((((...((.(.(((((..---..))))))))))))))..(((((((.......)))-)))).))).)))...(((......)-))------))))-) ( -35.10)
>consensus
UUUGCUGAC_GGAAUGCCAUGUUAGAUGGCAGCAAA___CAUGCCGCUCCAUGGCAAGAGUCG_GGCCAGGCCG_ACUUAAUUGCAUAUUUGCAUAGGCG_CA______CAGC_A
..............((((((.....))))))..........(((((((...((((..........)))))))..........((((....))))..))))............... (-13.30 = -14.22 +   0.92)

alignment

secondary structure

dotplot

Window 0

Location	20,353,476 – 20,353,577
Length	101
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	76.43
Mean single sequence MFE	-32.88
Consensus MFE	-13.78
Energy contribution	-13.90
Covariance contribution	0.12
Combinations/Pair	1.38
Mean z-score	-2.27
Structure conservation index	0.42
SVM decision value	0.58
SVM RNA-class probability	0.789600
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20353476 101 - 20766785
U-GCUC------UG-CGCCUAUGCAAAUAUGCAAUUAAGU-CGGCCUGGCC-CGACUCUUGCCAUCGAACGGCAUG---UUUGCUGCCAUCUAACAUGGCAUUCC-GUCAGCAAA
(-(((.------.(-((.....((((((((((.......(-(((..((((.-........))))))))...)))))---)))))((((((.....))))))...)-)).)))).. ( -32.10)
>DroPse_CAF1 82553 102 - 1
U-GCUG------UG-CGCCUAUGCAAAUAUGCAAUUAAGU-CAGCCUGGCCCCGACUCUUGCCAUGGAGCGGCAUG---UUUGCCGUCAUCUAACAUGGCAUUCC-AUCAGCAAA
(-((((------((-.......((((((((((......((-(.....)))..((.((((......)))))))))))---))))).(((((.....)))))....)-).))))).. ( -31.30)
>DroWil_CAF1 134481 105 - 1
---CUC------UCUUGCCUAUGCAAAUAUGCAAUUAACUUUGGCCUGAGC-CGGAGUUUGAGCCUGAGCGGCAUGUUGUUUGUUGCCAUCUAACAUGGCAUUCCAGUCAACAGU
---...------...((((..((((....))))...(((((((((....))-)))))))...((....))))))(((((.(((.((((((.....))))))...))).))))).. ( -32.80)
>DroMoj_CAF1 110049 90 - 1
UC---G------GC-UGGCUAUGCAAAUAUGCAAUUAG-------CUGGUC-AGCUUUUUGCCAUGGAGCGUCAUG---UUUGUUGCCAUCUAACAUGACAUUCC-AGCU---GA
((---(------((-(((....((...(((((((..((-------((....-))))..))).))))..))((((((---((.(.......).))))))))...))-))))---)) ( -34.10)
>DroAna_CAF1 69203 108 - 1
U-GCUUUUCUGGUG-CGCCUAUGCAAAUAUGCAAUUAAGU-CGGCCGGGCCCCGGCUCUUGCCAUCGAGCAGCGUG---UUUGCUGCCAUCUAACAUGGCAUUCC-GUCAGCAAG
(-(((....(((..-.......((((((((((........-.((((((...))))))..(((......))))))))---)))))((((((.....))))))..))-)..)))).. ( -35.70)
>DroPer_CAF1 82610 102 - 1
U-GCUG------UG-CGCCUAUGCAAAUAUGCAAUUAAGU-CAGCCUGGCCCCGACUCUUGCCAUGGAGCGGCAUG---UUUGCCGUCAUCUAACAUGGCAUUCC-AUCAGCAAA
(-((((------((-.......((((((((((......((-(.....)))..((.((((......)))))))))))---))))).(((((.....)))))....)-).))))).. ( -31.30)
>consensus
U_GCUG______UG_CGCCUAUGCAAAUAUGCAAUUAAGU_CGGCCUGGCC_CGACUCUUGCCAUGGAGCGGCAUG___UUUGCUGCCAUCUAACAUGGCAUUCC_AUCAGCAAA
................(((..((((....))))..............(((..........))).....((((((.......))))))..........)))............... (-13.78 = -13.90 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:37 2006