Locus 4653

Sequence ID 2L_DroMel_CAF1
Location 13,335,386 – 13,335,570
Length 184
Max. P 0.979564
window7353 window7354 window7355 window7356

overview

Window 3

Location 13,335,386 – 13,335,477
Length 91
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 84.68
Mean single sequence MFE -23.42
Consensus MFE -17.73
Energy contribution -17.82
Covariance contribution 0.09
Combinations/Pair 1.21
Mean z-score -2.42
Structure conservation index 0.76
SVM decision value 0.42
SVM RNA-class probability 0.731171
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13335386 91 - 22407834
CUGUGUGUCUAACGUUUUGUUGAUUGAUGGUUAACCAGAAAAUCAAUAUCACUAUGCUAAUGAGACU-GGCAUAAAUGCACAAACAUAUGUA-----
.(((((((.....((..((((((((..(((....)))...))))))))..))(((((((.......)-)))))).)))))))..........----- ( -23.70)
>DroVir_CAF1 62814 90 - 1
UUUUGUGUAUGGCGUUUUGUUGAUUGAUGGUUAA-CAGAAAAUCAAUAUCACUAUGCUAAUGAGACA-AGCACGA--GCACGAGCACGAGCACG---
..((((.(.((((((..((((((((..((.....-))...)))))))).....))))))...).)))-)((.((.--((....)).)).))...--- ( -22.10)
>DroEre_CAF1 48848 91 - 1
CUGUGUGUCUAACGUUUUGUUGAUUGAUGGUUAACCGGAAAAUCAAUAUCACUAUGCUAAUGAGACU-GGCAUAAAUGCACAAACAUAUGUA-----
.(((((((.....((..((((((((..(((....)))...))))))))..))(((((((.......)-)))))).)))))))..........----- ( -23.00)
>DroWil_CAF1 84483 92 - 1
AUAUAUGUAUACCGUUUUGUUGAUUGAUGGUUAACCAGAAAAUCAAUAUCACUAUGCUAAUGAGACUAGGCAUAAAUGCACAUACACAGACA-----
.(((.(((((...((..((((((((..(((....)))...))))))))..))((((((..........)))))).))))).)))........----- ( -20.00)
>DroYak_CAF1 48055 91 - 1
CUGUGUGUCUAACGUUUUGUUGAUUGAUGGUUAACCAGAAAAUCAAUAUCACUAUGCUAAUGAGACU-GGCAUAGAUGCACAAACAUAUGUG-----
.((((((((((..((..((((((((..(((....)))...))))))))..))..(((((.......)-))))))))))))))..........----- ( -27.80)
>DroAna_CAF1 48532 96 - 1
UUGUGUGUCCAACGUUUUGUUGAUUGACGGUUAGCCGGAAAAUCAAUAUCACUAUGCUAAUGAGACU-CACAUAAGUGCACAAACAUAUGUACACAG
.((((.(((((.(((..((((((((..(((....)))...)))))))).....)))....)).))).-))))...(((.(((......))).))).. ( -23.90)
>consensus
CUGUGUGUCUAACGUUUUGUUGAUUGAUGGUUAACCAGAAAAUCAAUAUCACUAUGCUAAUGAGACU_GGCAUAAAUGCACAAACAUAUGUA_____
...(((((.....((..((((((((..(((....)))...))))))))..))((((((..........))))))...)))))............... (-17.73 = -17.82 +   0.09)

alignment

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secondary structure

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Window 4

Location 13,335,405 – 13,335,506
Length 101
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.97
Mean single sequence MFE -26.93
Consensus MFE -17.62
Energy contribution -17.40
Covariance contribution -0.22
Combinations/Pair 1.17
Mean z-score -2.97
Structure conservation index 0.65
SVM decision value 1.84
SVM RNA-class probability 0.979564
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13335405 101 + 22407834
AUGCC-AG-------UCUCAUUAGCAUAGUGAUAUUGAUUUUCUGGUUAACCAUCAAUCAACAAAACGUUAGACACACAGGCCC---------CAGA--UUGCUAUGCAAUUGAGGCUCC
.....-((-------(((((...((((((..((.((((((...(((....)))..))))))..................(....---------)..)--)..))))))...))))))).. ( -26.50)
>DroVir_CAF1 62833 97 + 1
GUGCU-UG-------UCUCAUUAGCAUAGUGAUAUUGAUUUUCUG-UUAACCAUCAAUCAACAAAACGCCAUACACAAAA------------UGAGA--UUGCAAUGCAAUUGAGGCUUC
.....-.(-------(((((...((((.(..((.((.(((((.((-(.........................))).))))------------).)))--)..).))))...))))))... ( -18.51)
>DroGri_CAF1 165531 105 + 1
GUUCU-CGUUUUCAUUCUCAUUAGCAUUGCAAUAUUGAUUUCCUGGUUAACCAUCAAUCAACAAAACGACAGACACAAAA------------UUAGA--UUGCAAUGCAAUUGAGGCUUC
.....-.........(((((...((((((((((.((((((...(((....)))..)))))).....(....)........------------....)--)))))))))...))))).... ( -23.30)
>DroWil_CAF1 84502 107 + 1
AUGCCUAG-------UCUCAUUAGCAUAGUGAUAUUGAUUUUCUGGUUAACCAUCAAUCAACAAAACGGUAUACAUAUAUGUACAAAA----UGAGA--UUGCUAUGCAAUUGAGGCUCC
......((-------(((((...((((((..((.((((((...(((....)))..)))))).......(((((......)))))....----....)--)..))))))...))))))).. ( -29.50)
>DroAna_CAF1 48556 103 + 1
AUGUG-AG-------UCUCAUUAGCAUAGUGAUAUUGAUUUUCCGGCUAACCGUCAAUCAACAAAACGUUGGACACACAAACCA---------AAGAUAUUGCUAUGCAAUUGAGGCUAC
.....-((-------(((((...((((((..(((((((((...(((....)))..)))).........((((.........)))---------).)))))..))))))...))))))).. ( -31.70)
>DroPer_CAF1 62159 110 + 1
GUGCU-AG-------UCUCAUUAGCAUAGUGAUAUUGAUUUUCCGGUUAACCAUCAAUCAACAAAACGCCACUCACACAUGUAUGAGAUGUAUGAGA--UUGCUAUGCAAUUGAGGCUUC
.....-((-------(((((...((((((..((.((((((....((....))...))))))..........((((.((((.......)))).)))))--)..))))))...))))))).. ( -32.10)
>consensus
AUGCU_AG_______UCUCAUUAGCAUAGUGAUAUUGAUUUUCUGGUUAACCAUCAAUCAACAAAACGCCAGACACACAAG___________UGAGA__UUGCUAUGCAAUUGAGGCUUC
...............(((((...(((((((((..((((((...(((....)))..))))))......(.....).........................)))))))))...))))).... (-17.62 = -17.40 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,335,405 – 13,335,506
Length 101
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.97
Mean single sequence MFE -28.43
Consensus MFE -19.15
Energy contribution -18.90
Covariance contribution -0.25
Combinations/Pair 1.13
Mean z-score -2.55
Structure conservation index 0.67
SVM decision value 1.59
SVM RNA-class probability 0.966203
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13335405 101 - 22407834
GGAGCCUCAAUUGCAUAGCAA--UCUG---------GGGCCUGUGUGUCUAACGUUUUGUUGAUUGAUGGUUAACCAGAAAAUCAAUAUCACUAUGCUAAUGAGA-------CU-GGCAU
((.(((((((((((...))))--).))---------))))))...........((..((((((((..(((....)))...))))))))..)).((((((......-------.)-))))) ( -29.10)
>DroVir_CAF1 62833 97 - 1
GAAGCCUCAAUUGCAUUGCAA--UCUCA------------UUUUGUGUAUGGCGUUUUGUUGAUUGAUGGUUAA-CAGAAAAUCAAUAUCACUAUGCUAAUGAGA-------CA-AGCAC
...........(((.(((...--(((((------------((....((((((.(...((((((((..((.....-))...)))))))).).)))))).)))))))-------))-)))). ( -25.00)
>DroGri_CAF1 165531 105 - 1
GAAGCCUCAAUUGCAUUGCAA--UCUAA------------UUUUGUGUCUGUCGUUUUGUUGAUUGAUGGUUAACCAGGAAAUCAAUAUUGCAAUGCUAAUGAGAAUGAAAACG-AGAAC
.....((((...(((((((((--.....------------......(.....)....((((((((..(((....)))...)))))))))))))))))...))))..........-..... ( -25.70)
>DroWil_CAF1 84502 107 - 1
GGAGCCUCAAUUGCAUAGCAA--UCUCA----UUUUGUACAUAUAUGUAUACCGUUUUGUUGAUUGAUGGUUAACCAGAAAAUCAAUAUCACUAUGCUAAUGAGA-------CUAGGCAU
...((((...((((...))))--(((((----((.((((((....))))))..((..((((((((..(((....)))...))))))))..))......)))))))-------..)))).. ( -28.40)
>DroAna_CAF1 48556 103 - 1
GUAGCCUCAAUUGCAUAGCAAUAUCUU---------UGGUUUGUGUGUCCAACGUUUUGUUGAUUGACGGUUAGCCGGAAAAUCAAUAUCACUAUGCUAAUGAGA-------CU-CACAU
((((.((((...((((((........(---------(((.........)))).....((((((((..(((....)))...))))))))...))))))...)))).-------))-.)).. ( -27.20)
>DroPer_CAF1 62159 110 - 1
GAAGCCUCAAUUGCAUAGCAA--UCUCAUACAUCUCAUACAUGUGUGAGUGGCGUUUUGUUGAUUGAUGGUUAACCGGAAAAUCAAUAUCACUAUGCUAAUGAGA-------CU-AGCAC
..((.((((...(((((((..--.(((((((((.......)))))))))..))((..((((((((..(((....)))...))))))))..)))))))...)))).-------))-..... ( -35.20)
>consensus
GAAGCCUCAAUUGCAUAGCAA__UCUCA___________CUUGUGUGUCUAACGUUUUGUUGAUUGAUGGUUAACCAGAAAAUCAAUAUCACUAUGCUAAUGAGA_______CU_AGCAC
.....((((...((((((...........................((.....))...((((((((..(((....)))...))))))))...))))))...))))................ (-19.15 = -18.90 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,335,477 – 13,335,570
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.97
Mean single sequence MFE -29.80
Consensus MFE -17.88
Energy contribution -18.35
Covariance contribution 0.48
Combinations/Pair 1.19
Mean z-score -1.65
Structure conservation index 0.60
SVM decision value 0.25
SVM RNA-class probability 0.653820
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13335477 93 - 22407834
-----U-GC-ACAUAAAUUGCUGCAUG------CCA-ACAGGCGCUUUAAGGCAUUCGAGCAUGGCG--UGCUGCGGUUUGGAGCCUCAAUUGCAUAGCAA--UCUG---------GGGC
-----.-..-...((((((((.(((((------(((-....(((((....)))......)).)))))--))).))))))))..(((((((((((...))))--).))---------)))) ( -34.90)
>DroVir_CAF1 62904 93 - 1
-----U-GC-ACAUAAAUUGUUGCAUA------CCAAGCAGACGCUUUAAGGCAUUCGAGCAUGGCGUGUGCUGCGGUUUGAAGCCUCAAUUGCAUUGCAA--UCUCA------------
-----(-((-(....(((((..((..(------((.((((.(((((.....((......))..))))).))))..))).....))..)))))....)))).--.....------------ ( -28.90)
>DroGri_CAF1 165610 89 - 1
-----U-GC-ACAUAAAUUGUCGCAUA------ACAA----ACGCUUUAAGGCAUUCGAGCAUGGCGUGUGCUGCGGUUUGAAGCCUCAAUUGCAUUGCAA--UCUAA------------
-----(-((-(....(((((..((...------.(((----(((((....)))...(((((((.....))))).)))))))..))..)))))....)))).--.....------------ ( -23.00)
>DroWil_CAF1 84575 99 - 1
-----U-AU-ACAUAAAUUGUUGCAUA------CCAAGCAGGCGCUUUAAGGCAUUCGAGCAUGGCG--UGCUGCGGUUUGGAGCCUCAAUUGCAUAGCAA--UCUCA----UUUUGUAC
-----.-.(-(((((((((((.(((..------(((.((.((.(((....)))..))..)).)))..--))).))))))))(((.....(((((...))))--)))).----...)))). ( -24.90)
>DroAna_CAF1 48628 102 - 1
UGGCAU-GCAACAUAAAUUGUUGCAUG------CCAGGCAGGCGCUUUAAGGCAUUCGAGCAUGGCG--UGCUGCGGUUUGUAGCCUCAAUUGCAUAGCAAUAUCUU---------UGGU
((((((-((((((.....)))))))))------))).(((((((((.....((......))..))))--).))))(((.....)))...(((((...))))).....---------.... ( -39.50)
>DroPer_CAF1 62231 110 - 1
-----UGGG-ACAUAAAUUGUUGCAUACGCAUACCAAGCAGGCGCUUUAAGGCACUCGGGCGUAGCG--UGCUGCGGUUUGAAGCCUCAAUUGCAUAGCAA--UCUCAUACAUCUCAUAC
-----((((-(........(((((.((.(((......(.(((((((....)))..((((((((((..--..)))).)))))).)))))...))).))))))--)........)))))... ( -27.59)
>consensus
_____U_GC_ACAUAAAUUGUUGCAUA______CCAAGCAGGCGCUUUAAGGCAUUCGAGCAUGGCG__UGCUGCGGUUUGAAGCCUCAAUUGCAUAGCAA__UCUCA___________C
.................((((((((..........((((....))))..((((.(((((((..(((....)))...)))))))))))....))))..))))................... (-17.88 = -18.35 +   0.48)

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 11:23:45 2006