Locus 927

Sequence ID 2L_DroMel_CAF1
Location 2,664,402 – 2,664,522
Length 120
Max. P 0.999846
window1492 window1493 window1494 window1495

overview

Window 2

Location 2,664,402 – 2,664,492
Length 90
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 79.57
Mean single sequence MFE -20.84
Consensus MFE -10.91
Energy contribution -12.67
Covariance contribution 1.76
Combinations/Pair 1.24
Mean z-score -2.04
Structure conservation index 0.52
SVM decision value 0.42
SVM RNA-class probability 0.727555
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2664402 90 + 22407834
ACGUGUUCAUAUCCUUGUCAUCCUGCCGGUUGUAUGUGCACACACAUAUGUACAUAU----AUGUACAUAUAUACGGCGCACACACAGUAAGCU
........................((..(((((.(((((.(....(((((((((...----.))))))))).....).))))).)))))..)). ( -21.40)
>DroSec_CAF1 83345 78 + 1
ACGUGUUCAUAUCCUUGUCGUCCUGCCGUUUGUGUGUGCACACACAUAUGUA----U----UUGUACA----UACGGC----ACACAGUAAGCU
.............((((..((..(((((..((((((....))))))((((((----.----...))))----))))))----).))..)))).. ( -21.20)
>DroSim_CAF1 84472 78 + 1
ACGUGUUCAUAUCCUUGUCGUCCUGCCGUUUGUAUGUGCACACACAUAUGUA----U----CUGUACA----UACGGC----ACACAGUAAGCU
.............((((..((..((((((.((((((((((........))))----)----..)))))----.)))))----).))..)))).. ( -19.50)
>DroEre_CAF1 91735 90 + 1
ACGUGUUCAUAUCCUUGUCGUCCUGCCGUCUGUACGUGUGCACACAUAUACACAUAUACAAUUGUAUAUAUGUACGGC----ACACAGUAAGCU
.............((((..((..((((((.((((....)))).(((((((.(((........))).))))))))))))----).))..)))).. ( -20.80)
>DroYak_CAF1 87142 74 + 1
ACGUGUUCAUAUCCUUGUCGUCCUGCCGUCUGUAUGUGUGCACAUACA----------------UAUAUGUGCACGGC----ACACAGUAAGCU
(((....((......)).)))...((...((((.((((((((((((..----------------..))))))))).))----).))))...)). ( -21.30)
>consensus
ACGUGUUCAUAUCCUUGUCGUCCUGCCGUUUGUAUGUGCACACACAUAUGUA____U____UUGUACAU_U_UACGGC____ACACAGUAAGCU
..((((.((......)).......(((((.((((((((((......................)))))))))).)))))....))))........ (-10.91 = -12.67 +   1.76)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,664,402 – 2,664,492
Length 90
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 79.57
Mean single sequence MFE -25.06
Consensus MFE -13.20
Energy contribution -14.36
Covariance contribution 1.16
Combinations/Pair 1.23
Mean z-score -2.62
Structure conservation index 0.53
SVM decision value 1.72
SVM RNA-class probability 0.974141
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2664402 90 - 22407834
AGCUUACUGUGUGUGCGCCGUAUAUAUGUACAU----AUAUGUACAUAUGUGUGUGCACAUACAACCGGCAGGAUGACAAGGAUAUGAACACGU
.(((...(((((((((((.(((((((((((((.----...))))))))))))))))))))))))...)))........................ ( -32.20)
>DroSec_CAF1 83345 78 - 1
AGCUUACUGUGU----GCCGUA----UGUACAA----A----UACAUAUGUGUGUGCACACACAAACGGCAGGACGACAAGGAUAUGAACACGU
..(((..(((.(----((((((----((((...----.----))))).((((((....)))))).)))))).).))..)))............. ( -20.90)
>DroSim_CAF1 84472 78 - 1
AGCUUACUGUGU----GCCGUA----UGUACAG----A----UACAUAUGUGUGUGCACAUACAAACGGCAGGACGACAAGGAUAUGAACACGU
........((((----.(((((----(((.((.----(----(((....)))).)).))))))...((......))....))......)))).. ( -19.70)
>DroEre_CAF1 91735 90 - 1
AGCUUACUGUGU----GCCGUACAUAUAUACAAUUGUAUAUGUGUAUAUGUGUGCACACGUACAGACGGCAGGACGACAAGGAUAUGAACACGU
..(((..(((.(----(((((((((((((((....)))))))))).((((((....))))))...)))))).).))..)))............. ( -27.10)
>DroYak_CAF1 87142 74 - 1
AGCUUACUGUGU----GCCGUGCACAUAUA----------------UGUAUGUGCACACAUACAGACGGCAGGACGACAAGGAUAUGAACACGU
.(((..((((((----(..(((((((((..----------------..))))))))).)))))))..)))........................ ( -25.40)
>consensus
AGCUUACUGUGU____GCCGUA_A_AUGUACAA____A____UACAUAUGUGUGUGCACAUACAAACGGCAGGACGACAAGGAUAUGAACACGU
........((((....(((((...((((((............))))))((((((....)))))).))))).(.....)..........)))).. (-13.20 = -14.36 +   1.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,664,421 – 2,664,522
Length 101
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 77.39
Mean single sequence MFE -34.09
Consensus MFE -22.08
Energy contribution -22.96
Covariance contribution 0.88
Combinations/Pair 1.21
Mean z-score -3.18
Structure conservation index 0.65
SVM decision value 3.52
SVM RNA-class probability 0.999340
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2664421 101 + 22407834
AUCCUGCCGGUUGUAUGUGCACACACAUAUGUACAUAU----AUGUACAUAUAUACGGCGCACACACAGUAAGCUCACGCG------CGUGUGUGUGUGCACUGCACUUUG
........(((.(((.(((((((((((((((((((...----.)))))))))(((((.(((.................)))------)))))))))))))))))))))... ( -37.83)
>DroSec_CAF1 83364 89 + 1
GUCCUGCCGUUUGUGUGUGCACACACAUAUGUA----U----UUGUACA----UACGGC----ACACAGUAAGCUCACGAG------CGUGUGUGUGUGCACUGCACUUUG
............((((((((((((((((((((.----(----.((..(.----(((...----.....))).)..)).).)------))))))))))))))).)))).... ( -33.50)
>DroSim_CAF1 84491 89 + 1
GUCCUGCCGUUUGUAUGUGCACACACAUAUGUA----U----CUGUACA----UACGGC----ACACAGUAAGCUCACGCG------CGUGUGUGUGUGCACUGCACUUUG
...........((((.((((((((((((((((.----.----((((...----.)))).----.........((....)))------)))))))))))))))))))..... ( -32.60)
>DroEre_CAF1 91754 97 + 1
GUCCUGCCGUCUGUACGUGUGCACACAUAUACACAUAUACAAUUGUAUAUAUGUACGGC----ACACAGUAAGCUCACGCGU----------GUGUGUGCACUGCACUUUG
....(((.((...(((((((((..(((((((.(((........))).)))))))...))----)))).))).((.((((...----------.)))).)))).)))..... ( -29.80)
>DroYak_CAF1 87161 91 + 1
GUCCUGCCGUCUGUAUGUGUGCACAUACA----------------UAUAUGUGCACGGC----ACACAGUAAGCUCACGCGUGUGCGCGUGUGUGUGUGCACUGCACUUUG
....(((.((.......((((((((((..----------------..))))))))))((----((((.....((.((((((....)))))).)))))))))).)))..... ( -36.70)
>consensus
GUCCUGCCGUUUGUAUGUGCACACACAUAUGUA____U____UUGUACAU_U_UACGGC____ACACAGUAAGCUCACGCG______CGUGUGUGUGUGCACUGCACUUUG
...........((((.(((((((((((((((......................(((............))).((....)).......)))))))))))))))))))..... (-22.08 = -22.96 +   0.88)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,664,421 – 2,664,522
Length 101
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 77.39
Mean single sequence MFE -37.36
Consensus MFE -19.29
Energy contribution -20.45
Covariance contribution 1.16
Combinations/Pair 1.19
Mean z-score -4.40
Structure conservation index 0.52
SVM decision value 4.24
SVM RNA-class probability 0.999846
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2664421 101 - 22407834
CAAAGUGCAGUGCACACACACACG------CGCGUGAGCUUACUGUGUGUGCGCCGUAUAUAUGUACAU----AUAUGUACAUAUGUGUGUGCACAUACAACCGGCAGGAU
....((((((((((((((((....------.((....))....)))))))))))((((((((((((((.----...)))))))))))))))))))......((....)).. ( -44.30)
>DroSec_CAF1 83364 89 - 1
CAAAGUGCAGUGCACACACACACG------CUCGUGAGCUUACUGUGU----GCCGUA----UGUACAA----A----UACAUAUGUGUGUGCACACACAAACGGCAGGAC
....(((..((((((((((.((((------(..(((....))).))))----)..(((----((((...----.----))))))))))))))))).)))............ ( -31.50)
>DroSim_CAF1 84491 89 - 1
CAAAGUGCAGUGCACACACACACG------CGCGUGAGCUUACUGUGU----GCCGUA----UGUACAG----A----UACAUAUGUGUGUGCACAUACAAACGGCAGGAC
.....(((.((((((((((.((((------(((....)).....))))----)..(((----((((...----.----)))))))))))))))))...(....)))).... ( -32.90)
>DroEre_CAF1 91754 97 - 1
CAAAGUGCAGUGCACACAC----------ACGCGUGAGCUUACUGUGU----GCCGUACAUAUAUACAAUUGUAUAUGUGUAUAUGUGUGCACACGUACAGACGGCAGGAC
.....(((.((((((((((----------(((((((....))).))))----)..((((((((((((....)))))))))))).))))))))).(((....)))))).... ( -39.20)
>DroYak_CAF1 87161 91 - 1
CAAAGUGCAGUGCACACACACACGCGCACACGCGUGAGCUUACUGUGU----GCCGUGCACAUAUA----------------UGUAUGUGCACACAUACAGACGGCAGGAC
....((((...)))).....((((((....)))))).(((..((((((----(..(((((((((..----------------..))))))))).)))))))..)))..... ( -38.90)
>consensus
CAAAGUGCAGUGCACACACACACG______CGCGUGAGCUUACUGUGU____GCCGUA_A_AUGUACAA____A____UACAUAUGUGUGUGCACAUACAAACGGCAGGAC
....(..((((((.(((................))).))..))))..)....(((((...((((((............))))))((((((....)))))).)))))..... (-19.29 = -20.45 +   1.16)

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 09:48:57 2006