Locus 5942

Sequence ID	3L_DroMel_CAF1
Location	15,919,427 – 15,919,581
Length	154
Max. P	0.999978

overview

Window 8

Location	15,919,427 – 15,919,547
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.50
Mean single sequence MFE	-38.99
Consensus MFE	-33.10
Energy contribution	-33.34
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.41
Structure conservation index	0.85
SVM decision value	0.12
SVM RNA-class probability	0.592898
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15919427 120 + 23771897
CUGUUUCGGUUUUAAGCAAACAGCGAGCGCGCCUCUUUAACGGUUUUCGGGUGUUGCGUUCGCAUGUUUAUGCACGUUGAUUUCGCUGGCCGUUGUAAUAAAGGCCAACAAGGUCAGGUG
...............((((((((((((((((((((.............))).).))))))))).))))..)))((.(((((((.(.(((((...........))))).).))))))))). ( -36.12)
>DroSec_CAF1 21132 120 + 1
CUGUUUCGGUUUUAAGCAAACAACGAGUGCGCCUCUUUAACGGUUUUCGGGUGUUGCGUUCGCAUGUUUAUGCACGUUGAUUUCGCUGGCCGUUGUAAUAAAGGCCAACAAGGUCAGGUG
.((((((........).))))).......(((((...((((((((..((((....((((..((((....))))))))....))))..)))))))).......((((.....))))))))) ( -30.70)
>DroSim_CAF1 21451 120 + 1
CUGUUUCGGUUUUAAGCAAACAGCGAGCGCGCCUCUUUAACGGUUUUCGGGUGUUGCGUUCGCAUGUUUAUGCACGUUGAUUUCGCUGGCCGUUGUAAUAAAGGCCAACAAGGUCAGGUG
...............((((((((((((((((((((.............))).).))))))))).))))..)))((.(((((((.(.(((((...........))))).).))))))))). ( -36.12)
>DroEre_CAF1 18797 117 + 1
CUGUUUCGGUU-UAAGCAAACAGCGAGCGCG--UCUUUAACGGUUUUCGGGUGUUGCGUUCGCAUGUUUGUGCACGUUGAUUUUGUUGGCCGCUGUAAUAAAGGCCAACAAGGUCAGGUG
...........-...((((((((((((((((--.(.....((.....))...).))))))))).))))))).(((.(((((((((((((((...........)))))))))))))))))) ( -47.60)
>DroYak_CAF1 19370 119 + 1
CUGUUUCGGUU-UAAGCAAACAGCGAGCGCGCCUCUUUAACGGUUUUCGGGUGUUGCGUUCGCAUGUUUAUGCACGUUGAUUUUGUUGGCCGUUGUAAUAAAGGCCAACAAGGUCAGGUG
...........-...((((((((((((((((((((.............))).).))))))))).))))..)))((.(((((((((((((((...........))))))))))))))))). ( -44.42)
>consensus
CUGUUUCGGUUUUAAGCAAACAGCGAGCGCGCCUCUUUAACGGUUUUCGGGUGUUGCGUUCGCAUGUUUAUGCACGUUGAUUUCGCUGGCCGUUGUAAUAAAGGCCAACAAGGUCAGGUG
...............((((((((((((((((.(.((..((.....))..)).).))))))))).))))..)))((.(((((((.(.(((((...........))))).).))))))))). (-33.10 = -33.34 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	15,919,427 – 15,919,547
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.50
Mean single sequence MFE	-30.38
Consensus MFE	-29.18
Energy contribution	-28.98
Covariance contribution	-0.20
Combinations/Pair	1.12
Mean z-score	-1.67
Structure conservation index	0.96
SVM decision value	2.24
SVM RNA-class probability	0.990934
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15919427 120 - 23771897
CACCUGACCUUGUUGGCCUUUAUUACAACGGCCAGCGAAAUCAACGUGCAUAAACAUGCGAACGCAACACCCGAAAACCGUUAAAGAGGCGCGCUCGCUGUUUGCUUAAAACCGAAACAG
(((.(((..(((((((((...........)))))))))..)))..)))..((((((.((((.(((..(....)....((........)).))).))))))))))................ ( -30.80)
>DroSec_CAF1 21132 120 - 1
CACCUGACCUUGUUGGCCUUUAUUACAACGGCCAGCGAAAUCAACGUGCAUAAACAUGCGAACGCAACACCCGAAAACCGUUAAAGAGGCGCACUCGUUGUUUGCUUAAAACCGAAACAG
(((.(((..(((((((((...........)))))))))..)))..))).........((((..(((((...((.....)).....(((.....))))))))))))............... ( -27.50)
>DroSim_CAF1 21451 120 - 1
CACCUGACCUUGUUGGCCUUUAUUACAACGGCCAGCGAAAUCAACGUGCAUAAACAUGCGAACGCAACACCCGAAAACCGUUAAAGAGGCGCGCUCGCUGUUUGCUUAAAACCGAAACAG
(((.(((..(((((((((...........)))))))))..)))..)))..((((((.((((.(((..(....)....((........)).))).))))))))))................ ( -30.80)
>DroEre_CAF1 18797 117 - 1
CACCUGACCUUGUUGGCCUUUAUUACAGCGGCCAACAAAAUCAACGUGCACAAACAUGCGAACGCAACACCCGAAAACCGUUAAAGA--CGCGCUCGCUGUUUGCUUA-AACCGAAACAG
(((.(((..(((((((((...........)))))))))..)))..)))..((((((.((((.(((.......(.....)(((...))--)))).))))))))))....-........... ( -31.70)
>DroYak_CAF1 19370 119 - 1
CACCUGACCUUGUUGGCCUUUAUUACAACGGCCAACAAAAUCAACGUGCAUAAACAUGCGAACGCAACACCCGAAAACCGUUAAAGAGGCGCGCUCGCUGUUUGCUUA-AACCGAAACAG
(((.(((..(((((((((...........)))))))))..)))..)))..((((((.((((.(((..(....)....((........)).))).))))))))))....-........... ( -31.10)
>consensus
CACCUGACCUUGUUGGCCUUUAUUACAACGGCCAGCGAAAUCAACGUGCAUAAACAUGCGAACGCAACACCCGAAAACCGUUAAAGAGGCGCGCUCGCUGUUUGCUUAAAACCGAAACAG
(((.(((..(((((((((...........)))))))))..)))..)))..((((((.((((.(((.......(.....)(((.....)))))).))))))))))................ (-29.18 = -28.98 +  -0.20)

alignment

secondary structure

dotplot

Window 0

Location	15,919,467 – 15,919,581
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.88
Mean single sequence MFE	-47.42
Consensus MFE	-42.92
Energy contribution	-43.32
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-3.56
Structure conservation index	0.91
SVM decision value	4.50
SVM RNA-class probability	0.999911
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15919467 114 + 23771897
CGGUUUUCGGGUGUUGCGUUCGCAUGUUUAUGCACGUUGAUUUCGCUGGCCGUUGUAAUAAAGGCCAACAAGGUCAGGUGCAAACGAAAUGCGAGU------ACGAGUGACGCCUGCGUG
.......(((((((..(.(((((((.....(((((.(((((((.(.(((((...........))))).).))))))))))))......))))))).------....)..))))))).... ( -43.50)
>DroSec_CAF1 21172 114 + 1
CGGUUUUCGGGUGUUGCGUUCGCAUGUUUAUGCACGUUGAUUUCGCUGGCCGUUGUAAUAAAGGCCAACAAGGUCAGGUGCAAACGAAAUGCGAGU------ACGAGUGACGCCUGCGUG
.......(((((((..(.(((((((.....(((((.(((((((.(.(((((...........))))).).))))))))))))......))))))).------....)..))))))).... ( -43.50)
>DroSim_CAF1 21491 114 + 1
CGGUUUUCGGGUGUUGCGUUCGCAUGUUUAUGCACGUUGAUUUCGCUGGCCGUUGUAAUAAAGGCCAACAAGGUCAGGUGCAAACGAAAUGCGAGU------ACGAGUGACGCCUGCGUG
.......(((((((..(.(((((((.....(((((.(((((((.(.(((((...........))))).).))))))))))))......))))))).------....)..))))))).... ( -43.50)
>DroEre_CAF1 18834 114 + 1
CGGUUUUCGGGUGUUGCGUUCGCAUGUUUGUGCACGUUGAUUUUGUUGGCCGCUGUAAUAAAGGCCAACAAGGUCAGGUGCAAACGAAUUGCGAGU------ACGAGUGACGCCUGCGUG
.......(((((((..(.((((((.((((((((((.(((((((((((((((...........)))))))))))))))))))..)))))))))))).------....)..))))))).... ( -52.70)
>DroYak_CAF1 19409 120 + 1
CGGUUUUCGGGUGUUGCGUUCGCAUGUUUAUGCACGUUGAUUUUGUUGGCCGUUGUAAUAAAGGCCAACAAGGUCAGGUGCAAACGAAAUGCGAGUACGAGUACGAGUGACGCCUGCGUG
.......(((((((..(..((((((.....(((((.(((((((((((((((...........))))))))))))))))))))......))))))(((....)))..)..))))))).... ( -53.90)
>consensus
CGGUUUUCGGGUGUUGCGUUCGCAUGUUUAUGCACGUUGAUUUCGCUGGCCGUUGUAAUAAAGGCCAACAAGGUCAGGUGCAAACGAAAUGCGAGU______ACGAGUGACGCCUGCGUG
.......(((((((..(..((((((.....(((((.(((((((.(.(((((...........))))).).))))))))))))......))))))(((....)))..)..))))))).... (-42.92 = -43.32 +   0.40)

alignment

secondary structure

dotplot

Window 1

Location	15,919,467 – 15,919,581
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.88
Mean single sequence MFE	-33.94
Consensus MFE	-33.24
Energy contribution	-32.96
Covariance contribution	-0.28
Combinations/Pair	1.07
Mean z-score	-2.81
Structure conservation index	0.98
SVM decision value	5.18
SVM RNA-class probability	0.999978
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15919467 114 - 23771897
CACGCAGGCGUCACUCGU------ACUCGCAUUUCGUUUGCACCUGACCUUGUUGGCCUUUAUUACAACGGCCAGCGAAAUCAACGUGCAUAAACAUGCGAACGCAACACCCGAAAACCG
......((.((....(((------..((((((......(((((.(((..(((((((((...........)))))))))..)))..))))).....)))))))))....))))........ ( -33.90)
>DroSec_CAF1 21172 114 - 1
CACGCAGGCGUCACUCGU------ACUCGCAUUUCGUUUGCACCUGACCUUGUUGGCCUUUAUUACAACGGCCAGCGAAAUCAACGUGCAUAAACAUGCGAACGCAACACCCGAAAACCG
......((.((....(((------..((((((......(((((.(((..(((((((((...........)))))))))..)))..))))).....)))))))))....))))........ ( -33.90)
>DroSim_CAF1 21491 114 - 1
CACGCAGGCGUCACUCGU------ACUCGCAUUUCGUUUGCACCUGACCUUGUUGGCCUUUAUUACAACGGCCAGCGAAAUCAACGUGCAUAAACAUGCGAACGCAACACCCGAAAACCG
......((.((....(((------..((((((......(((((.(((..(((((((((...........)))))))))..)))..))))).....)))))))))....))))........ ( -33.90)
>DroEre_CAF1 18834 114 - 1
CACGCAGGCGUCACUCGU------ACUCGCAAUUCGUUUGCACCUGACCUUGUUGGCCUUUAUUACAGCGGCCAACAAAAUCAACGUGCACAAACAUGCGAACGCAACACCCGAAAACCG
......((.((....(((------..(((((.......(((((.(((..(((((((((...........)))))))))..)))..)))))......))))))))....))))........ ( -32.22)
>DroYak_CAF1 19409 120 - 1
CACGCAGGCGUCACUCGUACUCGUACUCGCAUUUCGUUUGCACCUGACCUUGUUGGCCUUUAUUACAACGGCCAACAAAAUCAACGUGCAUAAACAUGCGAACGCAACACCCGAAAACCG
.......((((.....(((....)))((((((......(((((.(((..(((((((((...........)))))))))..)))..))))).....))))))))))............... ( -35.80)
>consensus
CACGCAGGCGUCACUCGU______ACUCGCAUUUCGUUUGCACCUGACCUUGUUGGCCUUUAUUACAACGGCCAGCGAAAUCAACGUGCAUAAACAUGCGAACGCAACACCCGAAAACCG
...((..(((.....)))........((((((......(((((.(((..(((((((((...........)))))))))..)))..))))).....))))))..))............... (-33.24 = -32.96 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:43 2006