Locus 3669

Sequence ID 2L_DroMel_CAF1
Location 10,670,882 – 10,671,030
Length 148
Max. P 0.933291
window5791 window5792 window5793 window5794

overview

Window 1

Location 10,670,882 – 10,670,994
Length 112
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 80.98
Mean single sequence MFE -40.66
Consensus MFE -23.07
Energy contribution -23.12
Covariance contribution 0.06
Combinations/Pair 1.26
Mean z-score -2.08
Structure conservation index 0.57
SVM decision value 0.23
SVM RNA-class probability 0.646387
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10670882 112 + 22407834
GUGCGCCGGGUGGAGAAUCAUCGGGCCAAGCUCACGGCCAAUUUGGCCAAUUACCUGGCCAUGCAGCUGCAGCGCCAG---CAGCUCCGCCAACAGAUGCAGCAGCAAAUGAUGG--
(((.(((((((((.........((((...))))..((((.....))))..))))))))))))(.((((((.......)---))))).).(((.((..(((....)))..)).)))-- ( -43.70)
>DroVir_CAF1 3338 114 + 1
AUACGACGCGUAGAGAAUCACAGGGCCAAGCUGACGGCCAAUUUGGCCAGCUUCCUGGCCAUGCAGCUGCAGCGUCAG---CAGCUCCAGAAUCAAAUACAAAUGCAGACAACGCUU
.......((((...((.((...((((...(((((((.......(((((((....)))))))(((....))).))))))---).))))..)).)).........((....)))))).. ( -36.10)
>DroPse_CAF1 2083 112 + 1
AUCCGGCGGGUCGAGAACCACAAGGCAAAGCUGACGGCCAAUCUGGCCAGCUUCUUGGCCAUGCAGCUGCAGCGGCAG---CAGCUGCAGAACCAAAUCCAGUUGCAGAUGUCGC--
...(((((((((((((.((....))...((((...((((.....)))))))))))))))).((((((((..(((((..---..))))).((......))))))))))..))))).-- ( -44.70)
>DroGri_CAF1 2158 114 + 1
AUACGACGCGUUGAGAACCACAGGGCCAAGUUGACAGCCAAUUUGGCCAGUUUCCUGGCCAUGCAGCUGCAGCGCCAG---CAGUUCCAGAAUCAAAUACAAAUGCAGACAACGCUC
.......((((((..........(((...((((.((((.....(((((((....)))))))....))))))))))).(---((....................)))...)))))).. ( -37.15)
>DroMoj_CAF1 2210 117 + 1
AUACGACGCGUGGAGAAUCAACGGGCCAAGCUGACAGCCAAUUUGGCCAGCUUCCUGGCCAUGCAGCUGCAGCGUCAGCAGCAGCUCCAGAAUCAAAUUCAAAUGCAGACUCAACUA
.........((.(((........((((((((((...(((.....))))))))...))))).(((((((((.((....)).)))))....((((...))))...))))..))).)).. ( -38.70)
>DroPer_CAF1 2082 112 + 1
AUCCGGCGGGUCGAGAACCACAAGGCAAAGCUGACGGCCAAUCUGGCCAGCUUCUUGGCCAUGCAGCUGCAGCGGCAG---CAGCUGCAGAACCAAAUCCAAUUGCAGAUGUCGC--
...(((((((((((((.((....))...((((...((((.....)))))))))))))))).(((((((((.......)---))))))))....................))))).-- ( -43.60)
>consensus
AUACGACGCGUCGAGAACCACAGGGCCAAGCUGACGGCCAAUUUGGCCAGCUUCCUGGCCAUGCAGCUGCAGCGCCAG___CAGCUCCAGAAUCAAAUACAAAUGCAGACGACGC__
....((......(((........(((...((((.((((.....(((((((....)))))))....)))))))))))........))).....))....................... (-23.07 = -23.12 +   0.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,670,882 – 10,670,994
Length 112
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 80.98
Mean single sequence MFE -45.87
Consensus MFE -25.33
Energy contribution -24.87
Covariance contribution -0.47
Combinations/Pair 1.23
Mean z-score -2.18
Structure conservation index 0.55
SVM decision value 0.24
SVM RNA-class probability 0.650746
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10670882 112 - 22407834
--CCAUCAUUUGCUGCUGCAUCUGUUGGCGGAGCUG---CUGGCGCUGCAGCUGCAUGGCCAGGUAAUUGGCCAAAUUGGCCGUGAGCUUGGCCCGAUGAUUCUCCACCCGGCGCAC
--.((((...(((.((((((..(((..(((....))---)..))).)))))).))).((((((((...(((((.....)))))...)))))))).)))).................. ( -50.20)
>DroVir_CAF1 3338 114 - 1
AAGCGUUGUCUGCAUUUGUAUUUGAUUCUGGAGCUG---CUGACGCUGCAGCUGCAUGGCCAGGAAGCUGGCCAAAUUGGCCGUCAGCUUGGCCCUGUGAUUCUCUACGCGUCGUAU
..((((.(((.(((..............((.(((((---(.......)))))).)).(((((((..(.(((((.....))))).)..))))))).)))))).....))))....... ( -41.70)
>DroPse_CAF1 2083 112 - 1
--GCGACAUCUGCAACUGGAUUUGGUUCUGCAGCUG---CUGCCGCUGCAGCUGCAUGGCCAAGAAGCUGGCCAGAUUGGCCGUCAGCUUUGCCUUGUGGUUCUCGACCCGCCGGAU
--.(((...(..(((..((..(((((..((((((((---(.......)))))))))..)))))((((((((((.....))))...)))))).)))))..)...))).((....)).. ( -46.60)
>DroGri_CAF1 2158 114 - 1
GAGCGUUGUCUGCAUUUGUAUUUGAUUCUGGAACUG---CUGGCGCUGCAGCUGCAUGGCCAGGAAACUGGCCAAAUUGGCUGUCAACUUGGCCCUGUGGUUCUCAACGCGUCGUAU
((((((((..(((....))).........(((((..---(.((.((((((((((..(((((((....)))))))...)))))))......))))).)..))))))))))).)).... ( -48.00)
>DroMoj_CAF1 2210 117 - 1
UAGUUGAGUCUGCAUUUGAAUUUGAUUCUGGAGCUGCUGCUGACGCUGCAGCUGCAUGGCCAGGAAGCUGGCCAAAUUGGCUGUCAGCUUGGCCCGUUGAUUCUCCACGCGUCGUAU
..(..(((((.((....((((...)))).((.(((...(((((((((((....)).(((((((....)))))))....))).))))))..))))))).)))))..)........... ( -42.10)
>DroPer_CAF1 2082 112 - 1
--GCGACAUCUGCAAUUGGAUUUGGUUCUGCAGCUG---CUGCCGCUGCAGCUGCAUGGCCAAGAAGCUGGCCAGAUUGGCCGUCAGCUUUGCCUUGUGGUUCUCGACCCGCCGGAU
--.(((...(..(((..((..(((((..((((((((---(.......)))))))))..)))))((((((((((.....))))...)))))).)))))..)...))).((....)).. ( -46.60)
>consensus
__GCGUCAUCUGCAUUUGGAUUUGAUUCUGGAGCUG___CUGACGCUGCAGCUGCAUGGCCAGGAAGCUGGCCAAAUUGGCCGUCAGCUUGGCCCUGUGAUUCUCCACCCGUCGUAU
..(((.....))).........((((...(.(((((...(....)...))))).)..(((((((....(((((.....)))))....)))))))................))))... (-25.33 = -24.87 +  -0.47)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,670,922 – 10,671,030
Length 108
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 76.48
Mean single sequence MFE -34.42
Consensus MFE -19.82
Energy contribution -19.68
Covariance contribution -0.14
Combinations/Pair 1.20
Mean z-score -1.57
Structure conservation index 0.58
SVM decision value 0.23
SVM RNA-class probability 0.642225
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10670922 108 + 22407834
AUUUGGCCAAUUACCUGGCCAUGCAGCUGCAGCGCCAGCAGCUCCGCCAACAGAUGCAGCAGCAAAUGAUGG------AGGGUCUGCCGCCCAAUGUGCACCUGCCCCACGGAC
...((((((......)))))).((((.(((((((...((((..((.(((.((..(((....)))..)).)))------.))..)))))))......)))).))))......... ( -40.00)
>DroVir_CAF1 3378 114 + 1
AUUUGGCCAGCUUCCUGGCCAUGCAGCUGCAGCGUCAGCAGCUCCAGAAUCAAAUACAAAUGCAGACAACGCUUCAAUCAGCUUUGCCGCCUAAUGUCCACUUGCCCCAUAGAU
...(((((((....)))))))((.((((((.......)))))).))...............(((((((..((..(((......)))..))....))))....)))......... ( -28.10)
>DroPse_CAF1 2123 105 + 1
AUCUGGCCAGCUUCUUGGCCAUGCAGCUGCAGCGGCAGCAGCUGCAGAACCAAAUCCAGUUGCAGAUGUCGC------AG---CUUCCACCCAACGUCCACCUCCCCCACGGCC
....((((......((((...(((((((((.......)))))))))...))))....((((((.......))------))---)).........................)))) ( -35.00)
>DroGri_CAF1 2198 114 + 1
AUUUGGCCAGUUUCCUGGCCAUGCAGCUGCAGCGCCAGCAGUUCCAGAAUCAAAUACAAAUGCAGACAACGCUCCAAUCAGCUCUGCCGCCCAAUGUUCACUUGCCUCAUAUGC
...(((((((....)))))))((.((((((.......)))))).))((((...........(((((....(((......))))))))........))))............... ( -27.21)
>DroSec_CAF1 2250 108 + 1
AUUUGGCCAAUUACCUGGCCAUGCAGCUGCAGCGCCAGCAGCUCCGCCAGCAGAUGCAGCAGCAGAUGUUGG------AGGGUCUGCCGCCCAAUGUGCACCUGCCCCACGGAC
...((((((......)))))).((((.(((((((...((((..((.((((((..(((....)))..))))))------.))..)))))))......)))).))))......... ( -45.40)
>DroPer_CAF1 2122 105 + 1
AUCUGGCCAGCUUCUUGGCCAUGCAGCUGCAGCGGCAGCAGCUGCAGAACCAAAUCCAAUUGCAGAUGUCGC------AG---CUUCCACCCAACGUCCACCUCCCCCACGGCC
....((((......((((...(((((((((.......)))))))))...))))......((((.......))------))---...........................)))) ( -30.80)
>consensus
AUUUGGCCAGCUUCCUGGCCAUGCAGCUGCAGCGCCAGCAGCUCCAGAACCAAAUACAAAUGCAGAUGACGC______AGG_UCUGCCGCCCAAUGUCCACCUGCCCCACGGAC
...(((((((....)))))))((.((((((.......)))))).)).................................................................... (-19.82 = -19.68 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,670,922 – 10,671,030
Length 108
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 76.48
Mean single sequence MFE -45.97
Consensus MFE -24.51
Energy contribution -24.43
Covariance contribution -0.08
Combinations/Pair 1.27
Mean z-score -2.19
Structure conservation index 0.53
SVM decision value 1.23
SVM RNA-class probability 0.933291
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10670922 108 - 22407834
GUCCGUGGGGCAGGUGCACAUUGGGCGGCAGACCCU------CCAUCAUUUGCUGCUGCAUCUGUUGGCGGAGCUGCUGGCGCUGCAGCUGCAUGGCCAGGUAAUUGGCCAAAU
.........((((.((((.....(.((((((..((.------(((.((..(((....)))..)).))).))..)))))).)..)))).)))).(((((((....)))))))... ( -47.90)
>DroVir_CAF1 3378 114 - 1
AUCUAUGGGGCAAGUGGACAUUAGGCGGCAAAGCUGAUUGAAGCGUUGUCUGCAUUUGUAUUUGAUUCUGGAGCUGCUGACGCUGCAGCUGCAUGGCCAGGAAGCUGGCCAAAU
......(((((((((..(((....(((((((.(((......))).))).))))...)))))))).))))(.((((((.......)))))).).(((((((....)))))))... ( -43.10)
>DroPse_CAF1 2123 105 - 1
GGCCGUGGGGGAGGUGGACGUUGGGUGGAAG---CU------GCGACAUCUGCAACUGGAUUUGGUUCUGCAGCUGCUGCCGCUGCAGCUGCAUGGCCAAGAAGCUGGCCAGAU
((((..(..(.(((((..(((..(((....)---))------))).))))).)..)....((((((..(((((((((.......)))))))))..)))))).....)))).... ( -45.70)
>DroGri_CAF1 2198 114 - 1
GCAUAUGAGGCAAGUGAACAUUGGGCGGCAGAGCUGAUUGGAGCGUUGUCUGCAUUUGUAUUUGAUUCUGGAACUGCUGGCGCUGCAGCUGCAUGGCCAGGAAACUGGCCAAAU
(((..((.(((..(....)....(.((((((..(((((..(((((.((....))..))).))..)))..))..)))))).)))).))..))).(((((((....)))))))... ( -41.70)
>DroSec_CAF1 2250 108 - 1
GUCCGUGGGGCAGGUGCACAUUGGGCGGCAGACCCU------CCAACAUCUGCUGCUGCAUCUGCUGGCGGAGCUGCUGGCGCUGCAGCUGCAUGGCCAGGUAAUUGGCCAAAU
.(((((.((.((((((((......((((((((....------......)))))))))))))))))).)))))(((((.......)))))....(((((((....)))))))... ( -52.70)
>DroPer_CAF1 2122 105 - 1
GGCCGUGGGGGAGGUGGACGUUGGGUGGAAG---CU------GCGACAUCUGCAAUUGGAUUUGGUUCUGCAGCUGCUGCCGCUGCAGCUGCAUGGCCAAGAAGCUGGCCAGAU
((((.........(..((.(((((((....)---))------.)))).))..).......((((((..(((((((((.......)))))))))..)))))).....)))).... ( -44.70)
>consensus
GUCCGUGGGGCAGGUGGACAUUGGGCGGCAGA_CCU______GCGACAUCUGCAACUGCAUUUGAUUCUGGAGCUGCUGGCGCUGCAGCUGCAUGGCCAGGAAACUGGCCAAAU
..........((((((..((....((((.....................))))...)))))))).....(.((((((.......)))))).).(((((((....)))))))... (-24.51 = -24.43 +  -0.08)

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 10:58:19 2006