Locus 1691

Sequence ID 2L_DroMel_CAF1
Location 4,619,946 – 4,620,079
Length 133
Max. P 0.988589
window2700 window2701 window2702 window2703

overview

Window 0

Location 4,619,946 – 4,620,065
Length 119
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.04
Mean single sequence MFE -35.27
Consensus MFE -27.62
Energy contribution -28.28
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.72
Structure conservation index 0.78
SVM decision value 0.26
SVM RNA-class probability 0.656880
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4619946 119 + 22407834
UGGUCCUGGG-CAAUUUGCAGAGUGCGCUGUCACGAUUAAUAACGCUGUCAUAAUAACACUUUUCUGUGAUUGAUUUAAGACAAUUACAGAAAAGAGGAACACAGCGCUCACGUUUGAUG
..(((....(-(.....)).((((((..(((..((((..........))).........((((((((((((((........)))))))))))))).)..)))..))))))......))). ( -33.00)
>DroVir_CAF1 61565 117 + 1
U-GUUCGGCG-CAAUUUGCGCUUUGCGCUGUCACGAUUAAUAACGCUGUCAUAAUAACACUUUUCUGUGAUUGAUUUAAGACAAUUACAGAAAAGAGGAACACAGCGCUCACGUUUGAG-
.-((.(((((-(((........))))))))..)).........((((((........(.((((((((((((((........)))))))))))))).)....))))))((((....))))- ( -37.90)
>DroGri_CAF1 60181 118 + 1
U-GUUUGGCGGUAAUUUGCGCUGUGCGCUGUCACGAUUAAUAACGCUGUCAUAAUAACACUUUUCUGUGAUUGAUUUAAGACAAUUACAGAAAAGAGGAACACAGCGCUCACGUUUGAG-
.-.((..(((.......((((((((..(((.((((........)).)).).........((((((((((((((........)))))))))))))).))..))))))))...)))..)).- ( -36.80)
>DroWil_CAF1 54229 117 + 1
UUGUCCAUGG-CAAUUUGCGC--CGCGCUGUCACGAUUAAUAACGCUGUCAUAAUAACACUUUUCUGUGAUUGAUUUAAGACAAUUACAGAAAAGAGGAACACAGCGCUCACGUUUGUGG
....((((((-(.......))--)(((((((...(((..........))).........((((((((((((((........))))))))))))))......)))))))........)))) ( -36.30)
>DroMoj_CAF1 70847 117 + 1
U-GUUCGGCG-CAAUUUGCGCUUUGCGCUGUCACGAUUAAUAACGCUGUCAUAAUAACACUUUUCUGUGAUUGAUUUAAGACAAUUACAGAAAAGAGGAACACUGCGCUCACGUUUGAG-
(-((((((((-(((........)))))))(.((((........)).)).).........((((((((((((((........))))))))))))))..))))).....((((....))))- ( -33.90)
>DroPer_CAF1 63476 119 + 1
CAGUCUGGGG-CAAUUUGCAGAGUGCGCUGUCACGAUUAAUAACGCUGUCAUAAUAACACUUUUCUGUGAUUGAUUUAAGACAAUUACAGAAAAGAGGAACACAGCACUCACGUUUGAUG
..(((....(-(.....)).((((((..(((..((((..........))).........((((((((((((((........)))))))))))))).)..)))..))))))......))). ( -33.70)
>consensus
U_GUCCGGCG_CAAUUUGCGCUGUGCGCUGUCACGAUUAAUAACGCUGUCAUAAUAACACUUUUCUGUGAUUGAUUUAAGACAAUUACAGAAAAGAGGAACACAGCGCUCACGUUUGAG_
.................(((....(((((((...(((..........))).........((((((((((((((........))))))))))))))......)))))))...)))...... (-27.62 = -28.28 +   0.67)

alignment

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secondary structure

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Window 1

Location 4,619,946 – 4,620,065
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 92.04
Mean single sequence MFE -32.87
Consensus MFE -28.33
Energy contribution -28.13
Covariance contribution -0.19
Combinations/Pair 1.07
Mean z-score -2.75
Structure conservation index 0.86
SVM decision value 2.13
SVM RNA-class probability 0.988589
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4619946 119 - 22407834
CAUCAAACGUGAGCGCUGUGUUCCUCUUUUCUGUAAUUGUCUUAAAUCAAUCACAGAAAAGUGUUAUUAUGACAGCGUUAUUAAUCGUGACAGCGCACUCUGCAAAUUG-CCCAGGACCA
........(((.(((((((((..(.(((((((((.((((........)))).))))))))).)..))....)))))(((((.....))))).)).)))(((((.....)-)...)))... ( -30.30)
>DroVir_CAF1 61565 117 - 1
-CUCAAACGUGAGCGCUGUGUUCCUCUUUUCUGUAAUUGUCUUAAAUCAAUCACAGAAAAGUGUUAUUAUGACAGCGUUAUUAAUCGUGACAGCGCAAAGCGCAAAUUG-CGCCGAAC-A
-......((...(((((((((..(.(((((((((.((((........)))).))))))))).)..)).......(((........))).)))))))...((((.....)-)))))...-. ( -34.90)
>DroGri_CAF1 60181 118 - 1
-CUCAAACGUGAGCGCUGUGUUCCUCUUUUCUGUAAUUGUCUUAAAUCAAUCACAGAAAAGUGUUAUUAUGACAGCGUUAUUAAUCGUGACAGCGCACAGCGCAAAUUACCGCCAAAC-A
-...........(((((((((....(((((((((.((((........)))).)))))))))((((.....))))(((((((.....))))).)))))))))))...............-. ( -34.90)
>DroWil_CAF1 54229 117 - 1
CCACAAACGUGAGCGCUGUGUUCCUCUUUUCUGUAAUUGUCUUAAAUCAAUCACAGAAAAGUGUUAUUAUGACAGCGUUAUUAAUCGUGACAGCGCG--GCGCAAAUUG-CCAUGGACAA
(((.........(((((((((..(.(((((((((.((((........)))).))))))))).)..)).......(((........))).)))))))(--(((.....))-)).))).... ( -35.10)
>DroMoj_CAF1 70847 117 - 1
-CUCAAACGUGAGCGCAGUGUUCCUCUUUUCUGUAAUUGUCUUAAAUCAAUCACAGAAAAGUGUUAUUAUGACAGCGUUAUUAAUCGUGACAGCGCAAAGCGCAAAUUG-CGCCGAAC-A
-.......((..(((((((......(((((((((.((((........)))).)))))))))((((((.(((((...))))).....))))))((((...))))..))))-)))...))-. ( -32.80)
>DroPer_CAF1 63476 119 - 1
CAUCAAACGUGAGUGCUGUGUUCCUCUUUUCUGUAAUUGUCUUAAAUCAAUCACAGAAAAGUGUUAUUAUGACAGCGUUAUUAAUCGUGACAGCGCACUCUGCAAAUUG-CCCCAGACUG
........(((((((((((((..(.(((((((((.((((........)))).))))))))).)..))....)))(((((((.....))))).)))))))).))......-.......... ( -29.20)
>consensus
_CUCAAACGUGAGCGCUGUGUUCCUCUUUUCUGUAAUUGUCUUAAAUCAAUCACAGAAAAGUGUUAUUAUGACAGCGUUAUUAAUCGUGACAGCGCACAGCGCAAAUUG_CCCCGAAC_A
......(((..((((((((((..(.(((((((((.((((........)))).))))))))).)..))....))))))))......)))....(((.....)))................. (-28.33 = -28.13 +  -0.19)

alignment

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secondary structure

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Window 2

Location 4,619,985 – 4,620,079
Length 94
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 77.71
Mean single sequence MFE -29.65
Consensus MFE -22.23
Energy contribution -22.57
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.42
Structure conservation index 0.75
SVM decision value 1.94
SVM RNA-class probability 0.983405
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4619985 94 + 22407834
UAACGCUGUCAUAAUAACACUUUUCUGUGAUUGAUUUAAGACAAUUACAGAAAAGAGGAACACAGCGCUCACGUUUGAUGAUG-AGGAAUGGAGA----------------------
...((((((........(.((((((((((((((........)))))))))))))).)....))))))(((.(((((.......-..)))))))).---------------------- ( -28.10)
>DroPse_CAF1 71845 116 + 1
UAACGCUGUCAUAAUAACACUUUUCUGUGAUUGAUUUAAGACAAUUACAGAAAAGAGGAACACAGCGCUCACGUUUGAUGAUG-AGCAAUGGGCCGAGAUGGCCGCGAUGGGCUGAA
.....(((((.........((((((((((((((........)))))))))))))).........((((((((((...))).))-)))....((((.....)))))))))))...... ( -38.50)
>DroGri_CAF1 60220 79 + 1
UAACGCUGUCAUAAUAACACUUUUCUGUGAUUGAUUUAAGACAAUUACAGAAAAGAGGAACACAGCGCUCACGUUUGAG--------------------------------------
...((((((........(.((((((((((((((........)))))))))))))).)....))))))((((....))))-------------------------------------- ( -25.30)
>DroWil_CAF1 54266 106 + 1
UAACGCUGUCAUAAUAACACUUUUCUGUGAUUGAUUUAAGACAAUUACAGAAAAGAGGAACACAGCGCUCACGUUUGUGGAUGUAUGAAUAGA------UG-----GAUGGGUAGGA
....(((((........(.((((((((((((((........)))))))))))))).)....)))))((((((((((((..........)))))------))-----..))))).... ( -30.00)
>DroMoj_CAF1 70885 79 + 1
UAACGCUGUCAUAAUAACACUUUUCUGUGAUUGAUUUAAGACAAUUACAGAAAAGAGGAACACUGCGCUCACGUUUGAG--------------------------------------
...(((.............((((((((((((((........))))))))))))))((.....)))))((((....))))-------------------------------------- ( -21.30)
>DroPer_CAF1 63515 116 + 1
UAACGCUGUCAUAAUAACACUUUUCUGUGAUUGAUUUAAGACAAUUACAGAAAAGAGGAACACAGCACUCACGUUUGAUGAUG-AGCAAUGGGCCGAGAUGGCCGCGAUGGGCUGAA
...(((.(((((.......((((((((((((((........)))))))))))))).((..((..((.((((.......))).)-.))..))..))...))))).))).......... ( -34.70)
>consensus
UAACGCUGUCAUAAUAACACUUUUCUGUGAUUGAUUUAAGACAAUUACAGAAAAGAGGAACACAGCGCUCACGUUUGAGGAUG_AG_AAUGG_________________________
...((((((........(.((((((((((((((........)))))))))))))).)....)))))).................................................. (-22.23 = -22.57 +   0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,619,985 – 4,620,079
Length 94
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 77.71
Mean single sequence MFE -27.75
Consensus MFE -23.37
Energy contribution -23.40
Covariance contribution 0.03
Combinations/Pair 1.04
Mean z-score -3.83
Structure conservation index 0.84
SVM decision value 1.58
SVM RNA-class probability 0.965123
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4619985 94 - 22407834
----------------------UCUCCAUUCCU-CAUCAUCAAACGUGAGCGCUGUGUUCCUCUUUUCUGUAAUUGUCUUAAAUCAAUCACAGAAAAGUGUUAUUAUGACAGCGUUA
----------------------.........((-(((........)))))((((((((..(.(((((((((.((((........)))).))))))))).)..))....))))))... ( -25.20)
>DroPse_CAF1 71845 116 - 1
UUCAGCCCAUCGCGGCCAUCUCGGCCCAUUGCU-CAUCAUCAAACGUGAGCGCUGUGUUCCUCUUUUCUGUAAUUGUCUUAAAUCAAUCACAGAAAAGUGUUAUUAUGACAGCGUUA
....((.....))((((.....))))....(((-(((........))))))(((((((..(.(((((((((.((((........)))).))))))))).)..))....))))).... ( -36.00)
>DroGri_CAF1 60220 79 - 1
--------------------------------------CUCAAACGUGAGCGCUGUGUUCCUCUUUUCUGUAAUUGUCUUAAAUCAAUCACAGAAAAGUGUUAUUAUGACAGCGUUA
--------------------------------------..........((((((((((..(.(((((((((.((((........)))).))))))))).)..))....)))))))). ( -24.90)
>DroWil_CAF1 54266 106 - 1
UCCUACCCAUC-----CA------UCUAUUCAUACAUCCACAAACGUGAGCGCUGUGUUCCUCUUUUCUGUAAUUGUCUUAAAUCAAUCACAGAAAAGUGUUAUUAUGACAGCGUUA
...........-----..------..............(((....)))((((((((((..(.(((((((((.((((........)))).))))))))).)..))....)))))))). ( -26.50)
>DroMoj_CAF1 70885 79 - 1
--------------------------------------CUCAAACGUGAGCGCAGUGUUCCUCUUUUCUGUAAUUGUCUUAAAUCAAUCACAGAAAAGUGUUAUUAUGACAGCGUUA
--------------------------------------..........(((((.........(((((((((.((((........)))).)))))))))((((.....))))))))). ( -20.40)
>DroPer_CAF1 63515 116 - 1
UUCAGCCCAUCGCGGCCAUCUCGGCCCAUUGCU-CAUCAUCAAACGUGAGUGCUGUGUUCCUCUUUUCUGUAAUUGUCUUAAAUCAAUCACAGAAAAGUGUUAUUAUGACAGCGUUA
....((.....))((((.....))))....(((-(((........))))))(((((((..(.(((((((((.((((........)))).))))))))).)..))....))))).... ( -33.50)
>consensus
_________________________CCAUU_CU_CAUCAUCAAACGUGAGCGCUGUGUUCCUCUUUUCUGUAAUUGUCUUAAAUCAAUCACAGAAAAGUGUUAUUAUGACAGCGUUA
................................................((((((((((..(.(((((((((.((((........)))).))))))))).)..))....)))))))). (-23.37 = -23.40 +   0.03)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:32 2006