Locus 7228

Sequence ID 3R_DroMel_CAF1
Location 19,041,444 – 19,041,610
Length 166
Max. P 0.996840
window11696 window11697 window11698 window11699 window11700 window11701

overview

Window 6

Location 19,041,444 – 19,041,548
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.58
Mean single sequence MFE -32.88
Consensus MFE -20.88
Energy contribution -21.68
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.08
Structure conservation index 0.64
SVM decision value 0.56
SVM RNA-class probability 0.780167
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19041444 104 + 27905053
AGCUUCAUUU-----------UUUUG---CUGCGCCAGUCUGCGUGUUGAGGUCACACAUA--UGUACGCAAUGUGGCGACCUCUCUCACCCGAGAGAACAUAAAGACCAGGUAGAAAUC
.((..((...-----------...))---..))(((.((((..(((((((((((.(((((.--((....)))))))..))))))((((....)))).)))))..))))..)))....... ( -34.10)
>DroSec_CAF1 54056 107 + 1
AGCUUCAUUU-----------UUUUGCUGCUGCGCCAGUCUGCGUGUUGAGGUCACACAUA--UGUACGCAAUGUGGCGACCUCUCUCACCUGAGAGAACAUAAAGACCAGGUAGAAAUC
(((..((...-----------...))..)))..(((.((((..(((((((((((.(((((.--((....)))))))..))))))((((....)))).)))))..))))..)))....... ( -34.80)
>DroSim_CAF1 55751 107 + 1
AGCUUCAUUU-----------UUUUGCAGCUGCGACAGUCUGCGUGUUGAGGUCACACACA--UGUACGCAAUGUGGCGACCUCUCUCACCCGAGAGAACAUAAAGACCAGGUAGAAAUC
((((.((...-----------...)).))))...((.((((..(((((((((((.(.((((--(.......)))))).))))))((((....)))).)))))..))))...))....... ( -33.00)
>DroEre_CAF1 57009 102 + 1
AGCUUCAUUUUUGUU--UGUUUUUUGCU---GCGCCAGUCUGCGUGUUGAGGUCACACACA--UGUACGCAUUGUGGCGACCUCACUCACCUGAGAGAACAGAAAAACC-----------
.......((((((((--(..........---((((......))))..(((((((.((((.(--((....)))))))..)))))))(((....))).)))))))))....----------- ( -30.10)
>DroYak_CAF1 57377 120 + 1
AGCUUCAUUUCUGAUUUUUUUUUUUGCUUUUUUGCCAGUCUGCGUGUUGAGGUCACACACAUAUGUACGCAAUGUGGCGACCUCACUCACCCGAGAGAACAGUAAAACCAGGUAGACAUC
.........................((......))..((((((.((.(((((((.(.(((((.((....)))))))).)))))))(((......)))...........)).))))))... ( -32.40)
>consensus
AGCUUCAUUU___________UUUUGCU_CUGCGCCAGUCUGCGUGUUGAGGUCACACACA__UGUACGCAAUGUGGCGACCUCUCUCACCCGAGAGAACAUAAAGACCAGGUAGAAAUC
.....................................((((..(((((((((((.((((....((....)).))))..)))))).(((......))))))))..))))............ (-20.88 = -21.68 +   0.80)

alignment

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secondary structure

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Window 7

Location 19,041,444 – 19,041,548
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.58
Mean single sequence MFE -32.22
Consensus MFE -23.86
Energy contribution -24.62
Covariance contribution 0.76
Combinations/Pair 1.04
Mean z-score -1.62
Structure conservation index 0.74
SVM decision value 0.17
SVM RNA-class probability 0.616878
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19041444 104 - 27905053
GAUUUCUACCUGGUCUUUAUGUUCUCUCGGGUGAGAGAGGUCGCCACAUUGCGUACA--UAUGUGUGACCUCAACACGCAGACUGGCGCAG---CAAAA-----------AAAUGAAGCU
.........(..((((.(.(((((((......))))((((((((.((((((....))--.)))))))))))).))).).))))..).((..---((...-----------...))..)). ( -29.90)
>DroSec_CAF1 54056 107 - 1
GAUUUCUACCUGGUCUUUAUGUUCUCUCAGGUGAGAGAGGUCGCCACAUUGCGUACA--UAUGUGUGACCUCAACACGCAGACUGGCGCAGCAGCAAAA-----------AAAUGAAGCU
..((((...(..((((.(.((((.((((....))))((((((((.((((((....))--.)))))))))))))))).).))))..).((....))....-----------....)))).. ( -30.90)
>DroSim_CAF1 55751 107 - 1
GAUUUCUACCUGGUCUUUAUGUUCUCUCGGGUGAGAGAGGUCGCCACAUUGCGUACA--UGUGUGUGACCUCAACACGCAGACUGUCGCAGCUGCAAAA-----------AAAUGAAGCU
...........((.((((((..((((......))))(((((((((((((.......)--)))).)))))))).....((((.(((...)))))))....-----------..)))))))) ( -34.40)
>DroEre_CAF1 57009 102 - 1
-----------GGUUUUUCUGUUCUCUCAGGUGAGUGAGGUCGCCACAAUGCGUACA--UGUGUGUGACCUCAACACGCAGACUGGCGC---AGCAAAAAACA--AACAAAAAUGAAGCU
-----------.((((((((((.((.....(((..(((((((((((((.((....))--)))).)))))))))...))).....)).))---))..)))))).--............... ( -31.00)
>DroYak_CAF1 57377 120 - 1
GAUGUCUACCUGGUUUUACUGUUCUCUCGGGUGAGUGAGGUCGCCACAUUGCGUACAUAUGUGUGUGACCUCAACACGCAGACUGGCAAAAAAGCAAAAAAAAAAAUCAGAAAUGAAGCU
.........((((((((.......(((.(.(((..((((((((((((((((....)).))))).))))))))).))).))))...((......)).......)))))))).......... ( -34.90)
>consensus
GAUUUCUACCUGGUCUUUAUGUUCUCUCGGGUGAGAGAGGUCGCCACAUUGCGUACA__UGUGUGUGACCUCAACACGCAGACUGGCGCAG_AGCAAAA___________AAAUGAAGCU
.........(((((((...(((((((......))).(((((((((((..((....))...))).))))))))))))...))))))).................................. (-23.86 = -24.62 +   0.76)

alignment

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secondary structure

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Window 8

Location 19,041,470 – 19,041,577
Length 107
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 84.40
Mean single sequence MFE -36.96
Consensus MFE -25.39
Energy contribution -25.52
Covariance contribution 0.13
Combinations/Pair 1.07
Mean z-score -3.19
Structure conservation index 0.69
SVM decision value 2.07
SVM RNA-class probability 0.987070
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19041470 107 + 27905053
UGCGUGUUGAGGUCACACAUA--UGUACGCAAUGUGGCGACCUCUCUCACCCGAGAGAACAUAAAGACCAGGUAGAAAUC---UACCUGAUCUCUCCGGAGAGAGA---AUGUGA
.((((.....((((.(((((.--((....)))))))..))))((((((.((.((((((.(.....)..(((((((....)---)))))).)))))).)).))))))---)))).. ( -43.80)
>DroSec_CAF1 54085 102 + 1
UGCGUGUUGAGGUCACACAUA--UGUACGCAAUGUGGCGACCUCUCUCACCUGAGAGAACAUAAAGACCAGGUAGAAAUC---UAUCUGAUCUCUGCGGAGA--------GGUGA
...(((((((((((.(((((.--((....)))))))..))))))((((....)))).)))))......(((((((....)---))))))((((((....)))--------))).. ( -36.50)
>DroSim_CAF1 55780 105 + 1
UGCGUGUUGAGGUCACACACA--UGUACGCAAUGUGGCGACCUCUCUCACCCGAGAGAACAUAAAGACCAGGUAGAAAUC---UACCUGAUCUCUGCGGAGA--GA---AGGUGA
........((((((.(.((((--(.......)))))).))))))((((..((((((((.(.....)..(((((((....)---)))))).))))).))).))--))---...... ( -39.40)
>DroEre_CAF1 57044 89 + 1
UGCGUGUUGAGGUCACACACA--UGUACGCAUUGUGGCGACCUCACUCACCUGAGAGAACAGAAAAACC-------------------GAUCUCUGCGGAGA--GA---AGGUGA
...(((.(((((((.((((.(--((....)))))))..)))))))..)))(((......)))....(((-------------------..(((((....)))--))---.))).. ( -30.10)
>DroYak_CAF1 57417 113 + 1
UGCGUGUUGAGGUCACACACAUAUGUACGCAAUGUGGCGACCUCACUCACCCGAGAGAACAGUAAAACCAGGUAGACAUCAACUAGCUGAUCUCUGCGGAGA--GAAAAAGGUGA
...(((.(((((((.(.(((((.((....)))))))).)))))))..)))((((((((.((((........(....)........)))).))))).)))...--........... ( -34.99)
>consensus
UGCGUGUUGAGGUCACACACA__UGUACGCAAUGUGGCGACCUCUCUCACCCGAGAGAACAUAAAGACCAGGUAGAAAUC___UACCUGAUCUCUGCGGAGA__GA___AGGUGA
...(((..((((((.((((....((....)).))))..))))))...)))((((((((..........((((((.........)))))).))))).)))................ (-25.39 = -25.52 +   0.13)

alignment

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secondary structure

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Window 9

Location 19,041,470 – 19,041,577
Length 107
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 84.40
Mean single sequence MFE -40.21
Consensus MFE -26.99
Energy contribution -27.73
Covariance contribution 0.74
Combinations/Pair 1.07
Mean z-score -4.34
Structure conservation index 0.67
SVM decision value 2.76
SVM RNA-class probability 0.996840
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19041470 107 - 27905053
UCACAU---UCUCUCUCCGGAGAGAUCAGGUA---GAUUUCUACCUGGUCUUUAUGUUCUCUCGGGUGAGAGAGGUCGCCACAUUGCGUACA--UAUGUGUGACCUCAACACGCA
......---((((.(.((((((((((((((((---(....)))))))))).......)))).)))).))))((((((((.((((((....))--.))))))))))))........ ( -45.71)
>DroSec_CAF1 54085 102 - 1
UCACC--------UCUCCGCAGAGAUCAGAUA---GAUUUCUACCUGGUCUUUAUGUUCUCUCAGGUGAGAGAGGUCGCCACAUUGCGUACA--UAUGUGUGACCUCAACACGCA
(((((--------(....(((((((((((.((---(....))).))))))))..)))......))))))..((((((((.((((((....))--.))))))))))))........ ( -36.60)
>DroSim_CAF1 55780 105 - 1
UCACCU---UC--UCUCCGCAGAGAUCAGGUA---GAUUUCUACCUGGUCUUUAUGUUCUCUCGGGUGAGAGAGGUCGCCACAUUGCGUACA--UGUGUGUGACCUCAACACGCA
((((((---..--....((.((((((((((((---(....))))))))))))).)).......))))))..(((((((((((((.......)--)))).))))))))........ ( -46.42)
>DroEre_CAF1 57044 89 - 1
UCACCU---UC--UCUCCGCAGAGAUC-------------------GGUUUUUCUGUUCUCUCAGGUGAGUGAGGUCGCCACAAUGCGUACA--UGUGUGUGACCUCAACACGCA
((((((---..--.....(((((((..-------------------....)))))))......)))))).(((((((((((((.((....))--)))).)))))))))....... ( -34.12)
>DroYak_CAF1 57417 113 - 1
UCACCUUUUUC--UCUCCGCAGAGAUCAGCUAGUUGAUGUCUACCUGGUUUUACUGUUCUCUCGGGUGAGUGAGGUCGCCACAUUGCGUACAUAUGUGUGUGACCUCAACACGCA
..........(--((((((.(((((.(((((((..(....)...)))).....))).))))))))).)))((((((((((((((((....)).))))).)))))))))....... ( -38.20)
>consensus
UCACCU___UC__UCUCCGCAGAGAUCAGGUA___GAUUUCUACCUGGUCUUUAUGUUCUCUCGGGUGAGAGAGGUCGCCACAUUGCGUACA__UGUGUGUGACCUCAACACGCA
((((((...........((.(((((((((...............))))))))).)).......))))))..(((((((((((..((....))...))).))))))))........ (-26.99 = -27.73 +   0.74)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,041,508 – 19,041,610
Length 102
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 79.42
Mean single sequence MFE -30.92
Consensus MFE -15.53
Energy contribution -16.54
Covariance contribution 1.01
Combinations/Pair 1.11
Mean z-score -2.61
Structure conservation index 0.50
SVM decision value 1.68
SVM RNA-class probability 0.971638
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19041508 102 + 27905053
CCUCUCUCACCCGAGAGAACAUAAAGACCAGGUAGAAAUC---UACCUGAUCUCUCCGGAGAGAGA---AUGUGACACAUUAACUGAUACACC---UGUCCAAGAUGGAGG----
..((((((.((.((((((.(.....)..(((((((....)---)))))).)))))).)).))))))---.((((.((.......)).))))..---..(((.....)))..---- ( -33.50)
>DroSec_CAF1 54123 97 + 1
CCUCUCUCACCUGAGAGAACAUAAAGACCAGGUAGAAAUC---UAUCUGAUCUCUGCGGAGA--------GGUGACACAUUAACUGGUACACC---UGUCCAAGAUGGAGG----
((((((((....)))))).......((.(((((((....)---)))))).))(((..(((.(--------((((((.((.....)))).))))---).))).))).))...---- ( -34.50)
>DroSim_CAF1 55818 100 + 1
CCUCUCUCACCCGAGAGAACAUAAAGACCAGGUAGAAAUC---UACCUGAUCUCUGCGGAGA--GA---AGGUGACACAUUAACUGAUACACC---UGUCCAAGAUGGAGG----
(((((.((..((((((((.(.....)..(((((((....)---)))))).))))).))).((--..---(((((...((.....))...))))---).))...)).)))))---- ( -32.70)
>DroEre_CAF1 57082 88 + 1
CCUCACUCACCUGAGAGAACAGAAAAACC-------------------GAUCUCUGCGGAGA--GA---AGGUGACACAUCCACUGAGACACUUGCUGUCCAAGAUGGACGG---
.(((.(((.((..(((((...(......)-------------------..)))))..)).))--).---.((((.......))))))).......((((((.....))))))--- ( -23.50)
>DroYak_CAF1 57457 112 + 1
CCUCACUCACCCGAGAGAACAGUAAAACCAGGUAGACAUCAACUAGCUGAUCUCUGCGGAGA--GAAAAAGGUGACACAUCAAGUGAUACACCUG-UGUCCAAGUUGGAGGGUUC
((((.(((..((((((((.((((........(....)........)))).))))).))).))--)....(((((.(((.....)))...))))).-...........)))).... ( -30.39)
>consensus
CCUCUCUCACCCGAGAGAACAUAAAGACCAGGUAGAAAUC___UACCUGAUCUCUGCGGAGA__GA___AGGUGACACAUUAACUGAUACACC___UGUCCAAGAUGGAGG____
(((((.((..((((((((..........((((((.........)))))).))))).)))...........((((...((.....))...))))..........)).))))).... (-15.53 = -16.54 +   1.01)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,041,508 – 19,041,610
Length 102
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 79.42
Mean single sequence MFE -35.10
Consensus MFE -18.24
Energy contribution -18.86
Covariance contribution 0.62
Combinations/Pair 1.07
Mean z-score -2.85
Structure conservation index 0.52
SVM decision value 2.21
SVM RNA-class probability 0.990453
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19041508 102 - 27905053
----CCUCCAUCUUGGACA---GGUGUAUCAGUUAAUGUGUCACAU---UCUCUCUCCGGAGAGAUCAGGUA---GAUUUCUACCUGGUCUUUAUGUUCUCUCGGGUGAGAGAGG
----.........((((((---.((..........)).)))).))(---(((((((((((((((((((((((---(....)))))))))).......)))).)))).))))))). ( -39.61)
>DroSec_CAF1 54123 97 - 1
----CCUCCAUCUUGGACA---GGUGUACCAGUUAAUGUGUCACC--------UCUCCGCAGAGAUCAGAUA---GAUUUCUACCUGGUCUUUAUGUUCUCUCAGGUGAGAGAGG
----..........(((.(---((((.((((.....)).))))))--------).)))..(((((((((.((---(....))).)))))))))...(((((((....))))))). ( -34.80)
>DroSim_CAF1 55818 100 - 1
----CCUCCAUCUUGGACA---GGUGUAUCAGUUAAUGUGUCACCU---UC--UCUCCGCAGAGAUCAGGUA---GAUUUCUACCUGGUCUUUAUGUUCUCUCGGGUGAGAGAGG
----.((((((((.(((((---((((...((.....))...)))).---..--.......((((((((((((---(....))))))))))))).)))))....))))).)))... ( -37.70)
>DroEre_CAF1 57082 88 - 1
---CCGUCCAUCUUGGACAGCAAGUGUCUCAGUGGAUGUGUCACCU---UC--UCUCCGCAGAGAUC-------------------GGUUUUUCUGUUCUCUCAGGUGAGUGAGG
---.((((((.((.(((((.....))))).)))))))).....(((---((--((.((..(((((.(-------------------((.....))).)))))..)).))).)))) ( -32.10)
>DroYak_CAF1 57457 112 - 1
GAACCCUCCAACUUGGACA-CAGGUGUAUCACUUGAUGUGUCACCUUUUUC--UCUCCGCAGAGAUCAGCUAGUUGAUGUCUACCUGGUUUUACUGUUCUCUCGGGUGAGUGAGG
...............((((-((((((...))))...)))))).((((...(--((((((.(((((.(((((((..(....)...)))).....))).))))))))).))).)))) ( -31.30)
>consensus
____CCUCCAUCUUGGACA___GGUGUAUCAGUUAAUGUGUCACCU___UC__UCUCCGCAGAGAUCAGGUA___GAUUUCUACCUGGUCUUUAUGUUCUCUCGGGUGAGAGAGG
....(((((((((.(((((...((((...((.....))...))))...............(((((((((...............))))))))).)))))....)))))...)))) (-18.24 = -18.86 +   0.62)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:45 2006