Locus 1031

Sequence ID X_DroMel_CAF1
Location 3,015,705 – 3,015,859
Length 154
Max. P 0.975043
window1663 window1664 window1665 window1666 window1667

overview

Window 3

Location 3,015,705 – 3,015,798
Length 93
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 83.88
Mean single sequence MFE -28.23
Consensus MFE -19.70
Energy contribution -19.96
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.71
Structure conservation index 0.70
SVM decision value 1.74
SVM RNA-class probability 0.975043
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3015705 93 + 22224390
GUUCUCAGCAAUCAGGCGAAUGUUUCGACGCUUUUCGAUGAGAACGUUUCUUCGUUCGCCUAUCGAUAACCAGUUAUCGAUGAUGGUGAGUCA
...((((.((.(((((((((((....((((.(((((...)))))))))....)))))))))((((((((....)))))))))))).))))... ( -34.40)
>DroSec_CAF1 3520 89 + 1
GUUCUCAGCAAUCAGG--AACGUUUCGCUGCUUUCCGAUGAGAACGUUUCUUAG--CGCCUAUCGAUAACCAGUUAUCGAUGAUGGUAAGUCA
(((((((.......((--((.((......)).))))..)))))))....((((.--((..(((((((((....))))))))).)).))))... ( -26.50)
>DroSim_CAF1 3457 91 + 1
GUUCUCAGCAAUCAGGAGAACGUUUCGCCGCUUUCCGAUGAGAACGUUUCUUAG--CGCCUAUCGAUAACCAGUUAUCGAUGAUGGUGAGUCA
(((((((.......(((((.((......)).)))))..))))))).........--(((((((((((((....)))))))))..))))..... ( -28.60)
>DroEre_CAF1 3796 76 + 1
GUUCUCAGCAAUCAGCAGAACG---------------AUGAGAACGCUUCUCAG--CGCCUAUCGAUAACCAGUUAUCGAUGUUGGUGAUUCA
(((((..((.....)))))))(---------------((((((.....))))).--(((((((((((((....)))))))))..))))..)). ( -23.40)
>consensus
GUUCUCAGCAAUCAGGAGAACGUUUCGCCGCUUUCCGAUGAGAACGUUUCUUAG__CGCCUAUCGAUAACCAGUUAUCGAUGAUGGUGAGUCA
(((((((...............................)))))))...........(((((((((((((....)))))))))..))))..... (-19.70 = -19.96 +   0.25)

alignment

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secondary structure

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Window 4

Location 3,015,726 – 3,015,827
Length 101
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 80.92
Mean single sequence MFE -30.38
Consensus MFE -20.12
Energy contribution -20.92
Covariance contribution 0.80
Combinations/Pair 1.09
Mean z-score -1.75
Structure conservation index 0.66
SVM decision value 0.29
SVM RNA-class probability 0.669298
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3015726 101 + 22224390
G-UUUCGACGCUUUUCGAUGAGAACGUUUC--UUCGUUCGCCUAUCGAUAACCAGUUAUCGAUGAUGGUGAGUCAUGACUCAUGACUGGCCACGAGCCAAGUGG---
.-......(((((((((....(((((....--..)))))...(((((((((....))))))))).((((.(((((((...))))))).))))))))..))))).--- ( -36.60)
>DroSec_CAF1 3539 99 + 1
G-UUUCGCUGCUUUCCGAUGAGAACGUUUC--UUAG--CGCCUAUCGAUAACCAGUUAUCGAUGAUGGUAAGUCAUGACUCAUGACUGGCCACGAGCCAAGUGG---
.-...((((((((..((.(((((.....))--))).--))..(((((((((....))))))))).((((.(((((((...))))))).)))).))))..)))).--- ( -31.00)
>DroSim_CAF1 3478 99 + 1
G-UUUCGCCGCUUUCCGAUGAGAACGUUUC--UUAG--CGCCUAUCGAUAACCAGUUAUCGAUGAUGGUGAGUCAUGACUCAUGACUGGCCACGAGCCAAGUGG---
.-.....((((((.....(((((.....))--)))(--(...(((((((((....))))))))).((((.(((((((...))))))).))))...)).))))))--- ( -33.30)
>DroEre_CAF1 3817 84 + 1
G----------------AUGAGAACGCUUC--UCAG--CGCCUAUCGAUAACCAGUUAUCGAUGUUGGUGAUUCAUGACUCAUGACUGGCCACGAGCCAAGAGG---
.----------------.(((((.....))--))).--(((((((((((((....)))))))))..))))..(((((...))))).((((.....)))).....--- ( -24.80)
>DroAna_CAF1 3511 99 + 1
GCUUUUCACGCUUUCCGAUGAGAACGCUUCUCUCAG--CACCUAUCGAUAACCAGUUAUCGAUGCCGG------GUGAGUCAUGACUGGCCACGAGCCAAAAAAAAA
.........((((.(((.(((((.......))))).--....(((((((((....))))))))).)))------(((.((((....))))))))))).......... ( -26.20)
>consensus
G_UUUCGACGCUUUCCGAUGAGAACGUUUC__UUAG__CGCCUAUCGAUAACCAGUUAUCGAUGAUGGUGAGUCAUGACUCAUGACUGGCCACGAGCCAAGUGG___
.........................((((.............(((((((((....)))))))))..(((.(((((((...))))))).)))..)))).......... (-20.12 = -20.92 +   0.80)

alignment

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secondary structure

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Window 5

Location 3,015,726 – 3,015,827
Length 101
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 80.92
Mean single sequence MFE -29.98
Consensus MFE -20.52
Energy contribution -20.72
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.88
Structure conservation index 0.68
SVM decision value 0.61
SVM RNA-class probability 0.799980
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3015726 101 - 22224390
---CCACUUGGCUCGUGGCCAGUCAUGAGUCAUGACUCACCAUCAUCGAUAACUGGUUAUCGAUAGGCGAACGAA--GAAACGUUCUCAUCGAAAAGCGUCGAAA-C
---.....((((((((((....))))))))))((((.(.((...((((((((....)))))))).)).(((((..--....)))))..........).))))...-. ( -30.50)
>DroSec_CAF1 3539 99 - 1
---CCACUUGGCUCGUGGCCAGUCAUGAGUCAUGACUUACCAUCAUCGAUAACUGGUUAUCGAUAGGCG--CUAA--GAAACGUUCUCAUCGGAAAGCAGCGAAA-C
---...((((((((((((..(((((((...)))))))..)))).((((((((....)))))))).)).)--))))--)...((((((........)).))))...-. ( -29.70)
>DroSim_CAF1 3478 99 - 1
---CCACUUGGCUCGUGGCCAGUCAUGAGUCAUGACUCACCAUCAUCGAUAACUGGUUAUCGAUAGGCG--CUAA--GAAACGUUCUCAUCGGAAAGCGGCGAAA-C
---...((((((((((((..(((((((...)))))))..)))).((((((((....)))))))).)).)--))))--)...((((.((....)).))))......-. ( -31.10)
>DroEre_CAF1 3817 84 - 1
---CCUCUUGGCUCGUGGCCAGUCAUGAGUCAUGAAUCACCAACAUCGAUAACUGGUUAUCGAUAGGCG--CUGA--GAAGCGUUCUCAU----------------C
---..((.((((((((((....)))))))))).)).........((((((((....)))))))).((((--((..--..)))))).....----------------. ( -29.20)
>DroAna_CAF1 3511 99 - 1
UUUUUUUUUGGCUCGUGGCCAGUCAUGACUCAC------CCGGCAUCGAUAACUGGUUAUCGAUAGGUG--CUGAGAGAAGCGUUCUCAUCGGAAAGCGUGAAAAGC
.......(((((.....)))))(((((.(((((------(....((((((((....)))))))).))))--((((((((.....)))).))))..)))))))..... ( -29.40)
>consensus
___CCACUUGGCUCGUGGCCAGUCAUGAGUCAUGACUCACCAUCAUCGAUAACUGGUUAUCGAUAGGCG__CUAA__GAAACGUUCUCAUCGGAAAGCGGCGAAA_C
........((((((((((....)))))))))).......((...((((((((....)))))))).))........................................ (-20.52 = -20.72 +   0.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,015,763 – 3,015,859
Length 96
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 83.42
Mean single sequence MFE -31.02
Consensus MFE -20.22
Energy contribution -21.42
Covariance contribution 1.20
Combinations/Pair 1.04
Mean z-score -1.93
Structure conservation index 0.65
SVM decision value -0.05
SVM RNA-class probability 0.505752
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3015763 96 + 22224390
CCUAUCGAUAACCAGUUAUCGAUGAUGGUGAGUCAUGACUCAUGACUGGCCACGAGCCAAGUGG---GGGAGGAGAG------ACCGAAAUAGUCGCCCACGCCG-
..(((((((((....))))))))).((((.(((((((...))))))).))))((.((...((((---(.((((....------.)).......)).)))))))))- ( -35.11)
>DroSec_CAF1 3574 95 + 1
CCUAUCGAUAACCAGUUAUCGAUGAUGGUAAGUCAUGACUCAUGACUGGCCACGAGCCAAGUGG----GGAGGGGAG------AAUGAAAUAGUCGCCCACGCCG-
(((((((((((....))))))))).((((.(((((((...))))))).))))..........))----((..(((.(------(.........)).)))...)).- ( -30.80)
>DroSim_CAF1 3513 95 + 1
CCUAUCGAUAACCAGUUAUCGAUGAUGGUGAGUCAUGACUCAUGACUGGCCACGAGCCAAGUGG----GGAGGGGAG------AAUGGAAUAGUCGCCCACGCCG-
(((((((((((....))))))))).((((.(((((((...))))))).))))..........))----((..(((.(------(.........)).)))...)).- ( -32.90)
>DroEre_CAF1 3837 87 + 1
CCUAUCGAUAACCAGUUAUCGAUGUUGGUGAUUCAUGACUCAUGACUGGCCACGAGCCAAGAGG----G--------------AAAGAAAUAGUCGCCCACGCCG-
..(((((((((....)))))))))..((((..(((((...))))).((((.....))))...((----(--------------...((.....)).))).)))).- ( -26.10)
>DroYak_CAF1 3630 101 + 1
CCUAUCGAUAACCAGUUAUCGAUGAUGGUGAGUCAUGACUCAUGACUGGCCACGAGCCAAGUGG----GGAGGGGACGGCGGUAAAGAAAUAGUCGCCCACGCCG-
(((((((((((....))))))))).((((.(((((((...))))))).))))..........))----((..(((.((((............)))))))...)).- ( -38.00)
>DroAna_CAF1 3549 94 + 1
CCUAUCGAUAACCAGUUAUCGAUGCCGG------GUGAGUCAUGACUGGCCACGAGCCAAAAAAAAAUAAAGGAAAA------AAUUAAAUAGUCGCCCACACAGU
..(((((((((....)))))))))..((------((((((....))((((.....))))..................------..........))))))....... ( -23.20)
>consensus
CCUAUCGAUAACCAGUUAUCGAUGAUGGUGAGUCAUGACUCAUGACUGGCCACGAGCCAAGUGG____GGAGGGGAG______AAUGAAAUAGUCGCCCACGCCG_
..(((((((((....)))))))))..(((((((((((...))))))((((.....))))..................................)))))........ (-20.22 = -21.42 +   1.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,015,763 – 3,015,859
Length 96
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 83.42
Mean single sequence MFE -28.59
Consensus MFE -25.15
Energy contribution -24.90
Covariance contribution -0.25
Combinations/Pair 1.08
Mean z-score -1.42
Structure conservation index 0.88
SVM decision value 0.17
SVM RNA-class probability 0.618697
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3015763 96 - 22224390
-CGGCGUGGGCGACUAUUUCGGU------CUCUCCUCCC---CCACUUGGCUCGUGGCCAGUCAUGAGUCAUGACUCACCAUCAUCGAUAACUGGUUAUCGAUAGG
-.((.(((((.((.......((.------....)))).)---)))).((((((((((....)))))))))).......))...((((((((....))))))))... ( -31.21)
>DroSec_CAF1 3574 95 - 1
-CGGCGUGGGCGACUAUUUCAUU------CUCCCCUCC----CCACUUGGCUCGUGGCCAGUCAUGAGUCAUGACUUACCAUCAUCGAUAACUGGUUAUCGAUAGG
-.((.(((((.((..........------......)))----)))).((((((((((....)))))))))).......))...((((((((....))))))))... ( -30.29)
>DroSim_CAF1 3513 95 - 1
-CGGCGUGGGCGACUAUUCCAUU------CUCCCCUCC----CCACUUGGCUCGUGGCCAGUCAUGAGUCAUGACUCACCAUCAUCGAUAACUGGUUAUCGAUAGG
-.((.(((((.((..........------......)))----)))).((((((((((....)))))))))).......))...((((((((....))))))))... ( -30.29)
>DroEre_CAF1 3837 87 - 1
-CGGCGUGGGCGACUAUUUCUUU--------------C----CCUCUUGGCUCGUGGCCAGUCAUGAGUCAUGAAUCACCAACAUCGAUAACUGGUUAUCGAUAGG
-.((.((((....)))).))...--------------.----((((.((((((((((....)))))))))).)).........((((((((....)))))))).)) ( -27.10)
>DroYak_CAF1 3630 101 - 1
-CGGCGUGGGCGACUAUUUCUUUACCGCCGUCCCCUCC----CCACUUGGCUCGUGGCCAGUCAUGAGUCAUGACUCACCAUCAUCGAUAACUGGUUAUCGAUAGG
-.((.(.(((.(((...............)))))).).----)).(.((((((((((....)))))))))).)..........((((((((....))))))))... ( -31.66)
>DroAna_CAF1 3549 94 - 1
ACUGUGUGGGCGACUAUUUAAUU------UUUUCCUUUAUUUUUUUUUGGCUCGUGGCCAGUCAUGACUCAC------CCGGCAUCGAUAACUGGUUAUCGAUAGG
.(((.((((((((((...(((..------.......))).........(((.....)))))))..).)))))------.))).((((((((....))))))))... ( -21.00)
>consensus
_CGGCGUGGGCGACUAUUUCAUU______CUCCCCUCC____CCACUUGGCUCGUGGCCAGUCAUGAGUCAUGACUCACCAUCAUCGAUAACUGGUUAUCGAUAGG
..((.((((....)))).))...........................((((((((((....))))))))))............((((((((....))))))))... (-25.15 = -24.90 +  -0.25)

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 09:59:46 2006