Locus 2700

Sequence ID	3L_DroMel_CAF1
Location	7,540,373 – 7,540,573
Length	200
Max. P	0.999958

overview

Window 8

Location	7,540,373 – 7,540,493
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.92
Mean single sequence MFE	-44.88
Consensus MFE	-41.20
Energy contribution	-41.24
Covariance contribution	0.04
Combinations/Pair	1.14
Mean z-score	-1.99
Structure conservation index	0.92
SVM decision value	2.95
SVM RNA-class probability	0.997868
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7540373 120 - 23771897
GGGACAGGCGCACUGAAAGCCACCAGGCUCGUUCUGGCAAAAGUGGGAGCAAUUCCCAUUGGCCAGAGAGCACUCAUCAAUGUCCAAGCAUGUAUGCGCUGAUGGGGUUUCGGAUGAGGU
((....(((.........))).))..((((..((((((...((((((((...)))))))).)))))))))).((((((....(((.(((........)))....))).....)))))).. ( -45.00)
>DroSec_CAF1 9582 120 - 1
GGGACAGGCGCACUGAAAGCCACCUGGUUCAUUCUGACAAAAGUGGGAGCAAUUCCCAUUGGACAGAGAGCACUCAUCAAUGUCCAAGCAUGUAGGCGCUGAUGGGGCUUCGGAUGAGGU
......(((.........)))((((.((((..((((.(...((((((((...)))))))).).))))((((.(((((((.((((..........)))).))))))))))).)))).)))) ( -42.10)
>DroSim_CAF1 9491 120 - 1
GGGACAGGCGCACUGAAAGCCACCUGGCUCAUUCUGACAAAAGUGGGAGCAAUUCCCAUUGGACAGAGAGCACUCAUCAAUGUCCAAGCAUGUAGGCGCUGAUGGGGCUUCGGAUGAGGU
....((((.((.......))..))))((((..((((.(...((((((((...)))))))).).)))))))).((((((...((((.(((........)))....))))....)))))).. ( -42.40)
>DroEre_CAF1 9699 120 - 1
AGGACAGGCGCACAGGAAGCCACCUGGCUCAUUCUGGCAAAAGUGGGAGCAAUUCCCAUUGGCCAGGGAGCACUCAUCAAUGUCCAAGCAUGCAGGCGGAGAUGGGGCAUCGGAUGAGGU
....((((.((.......))..))))((((...(((((...((((((((...)))))))).))))).)))).((((((.((((((..((......)).......))))))..)))))).. ( -48.00)
>DroYak_CAF1 9587 120 - 1
AGGACAGGCGCACUGGAAGCCACCUGGCUCAUUCUGGCAAAAGUGGGAGCAAUUCCCAUUGGCCAGCGAGCACUCAUCAAUGUCCAAGCAUGUAGGCGGAGAUGGGACAUCGGGUGAGGU
....((((.((.......))..))))((((...(((((...((((((((...)))))))).))))).)))).((((((.((((((..((......)).......))))))..)))))).. ( -46.90)
>consensus
GGGACAGGCGCACUGAAAGCCACCUGGCUCAUUCUGGCAAAAGUGGGAGCAAUUCCCAUUGGCCAGAGAGCACUCAUCAAUGUCCAAGCAUGUAGGCGCUGAUGGGGCUUCGGAUGAGGU
....((((.((.......))..))))((((..((((((...((((((((...)))))))).)))))))))).((((((...((((..((......)).......))))....)))))).. (-41.20 = -41.24 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	7,540,413 – 7,540,533
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.08
Mean single sequence MFE	-45.42
Consensus MFE	-37.98
Energy contribution	-37.78
Covariance contribution	-0.20
Combinations/Pair	1.11
Mean z-score	-1.96
Structure conservation index	0.84
SVM decision value	1.69
SVM RNA-class probability	0.972452
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7540413 120 + 23771897
UUGAUGAGUGCUCUCUGGCCAAUGGGAAUUGCUCCCACUUUUGCCAGAACGAGCCUGGUGGCUUUCAGUGCGCCUGUCCCUUGGGCUAUGCCCUAUCCGAGGAUAUGCGCACCUGUCAGG
...((.((.((((((((((.(((((((.....)))))..)).))))))..)))))).))..((..((((((((.((((((..((((...)))).....).))))).))))).)))..)). ( -48.10)
>DroSec_CAF1 9622 120 + 1
UUGAUGAGUGCUCUCUGUCCAAUGGGAAUUGCUCCCACUUUUGUCAGAAUGAACCAGGUGGCUUUCAGUGCGCCUGUCCCUUGGGCCAUGCUCUAUCCGAGGAUAUGCGCACCUGUCAGG
(((((..((((.....((((((.((((...((...(((((...((.....))...)))))((.......))))...))))))))))...((..((((....)))).))))))..))))). ( -38.90)
>DroSim_CAF1 9531 120 + 1
UUGAUGAGUGCUCUCUGUCCAAUGGGAAUUGCUCCCACUUUUGUCAGAAUGAGCCAGGUGGCUUUCAGUGCGCCUGUCCCUUGGGCUAUGCUCUAUCCGAGGAUAUGCGCACCUGUCAGG
(((((..((((.....((((((.((((...((((...((......))...))))((((((((.....)).))))))))))))))))...((..((((....)))).))))))..))))). ( -42.50)
>DroEre_CAF1 9739 120 + 1
UUGAUGAGUGCUCCCUGGCCAAUGGGAAUUGCUCCCACUUUUGCCAGAAUGAGCCAGGUGGCUUCCUGUGCGCCUGUCCUUUGGGAUAUGCCUUAUCAGAGGACAUGCGCACCUGCCAGG
.......(.((((.(((((.(((((((.....)))))..)).)))))...)))))...((((.....((((((.((((((((((...........)))))))))).))))))..)))).. ( -50.10)
>DroYak_CAF1 9627 120 + 1
UUGAUGAGUGCUCGCUGGCCAAUGGGAAUUGCUCCCACUUUUGCCAGAAUGAGCCAGGUGGCUUCCAGUGCGCCUGUCCUUUGGGAUAUGCUUUAUCAGAGGAUAUGCGCACCUGUCAGG
(((((..(.((((.(((((.(((((((.....)))))..)).)))))...))))).((......)).((((((.((((((((((...........)))))))))).))))))..))))). ( -47.50)
>consensus
UUGAUGAGUGCUCUCUGGCCAAUGGGAAUUGCUCCCACUUUUGCCAGAAUGAGCCAGGUGGCUUUCAGUGCGCCUGUCCCUUGGGCUAUGCUCUAUCCGAGGAUAUGCGCACCUGUCAGG
.......(.((((.(((((.(((((((.....)))))..)).)))))...)))))...((((.....((((((.(((((...(((.....))).......))))).))))))..)))).. (-37.98 = -37.78 +  -0.20)

alignment

secondary structure

dotplot

Window 0

Location	7,540,413 – 7,540,533
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.08
Mean single sequence MFE	-45.48
Consensus MFE	-41.58
Energy contribution	-41.78
Covariance contribution	0.20
Combinations/Pair	1.11
Mean z-score	-3.04
Structure conservation index	0.91
SVM decision value	4.87
SVM RNA-class probability	0.999958
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7540413 120 - 23771897
CCUGACAGGUGCGCAUAUCCUCGGAUAGGGCAUAGCCCAAGGGACAGGCGCACUGAAAGCCACCAGGCUCGUUCUGGCAAAAGUGGGAGCAAUUCCCAUUGGCCAGAGAGCACUCAUCAA
..(((..(((((((.((((....))))((((...)))).........)))))))............((((..((((((...((((((((...)))))))).)))))))))).....))). ( -48.60)
>DroSec_CAF1 9622 120 - 1
CCUGACAGGUGCGCAUAUCCUCGGAUAGAGCAUGGCCCAAGGGACAGGCGCACUGAAAGCCACCUGGUUCAUUCUGACAAAAGUGGGAGCAAUUCCCAUUGGACAGAGAGCACUCAUCAA
..(((..(((((((.((((....))))..)).((..(((.((....(((.........))).)))))..))(((((.(...((((((((...)))))))).).))))).)))))..))). ( -39.80)
>DroSim_CAF1 9531 120 - 1
CCUGACAGGUGCGCAUAUCCUCGGAUAGAGCAUAGCCCAAGGGACAGGCGCACUGAAAGCCACCUGGCUCAUUCUGACAAAAGUGGGAGCAAUUCCCAUUGGACAGAGAGCACUCAUCAA
..(((((((((.((.((((....))))(.((....((....))....)).).......))))))))((((..((((.(...((((((((...)))))))).).)))))))).....))). ( -41.40)
>DroEre_CAF1 9739 120 - 1
CCUGGCAGGUGCGCAUGUCCUCUGAUAAGGCAUAUCCCAAAGGACAGGCGCACAGGAAGCCACCUGGCUCAUUCUGGCAAAAGUGGGAGCAAUUCCCAUUGGCCAGGGAGCACUCAUCAA
..((((..((((((.((((((..((((.....))))....)))))).)))))).....))))....((((...(((((...((((((((...)))))))).))))).))))......... ( -51.80)
>DroYak_CAF1 9627 120 - 1
CCUGACAGGUGCGCAUAUCCUCUGAUAAAGCAUAUCCCAAAGGACAGGCGCACUGGAAGCCACCUGGCUCAUUCUGGCAAAAGUGGGAGCAAUUCCCAUUGGCCAGCGAGCACUCAUCAA
..(((((((((.((...(((..((.....((...(((....)))...)).))..))).))))))))((((...(((((...((((((((...)))))))).))))).)))).....))). ( -45.80)
>consensus
CCUGACAGGUGCGCAUAUCCUCGGAUAGAGCAUAGCCCAAGGGACAGGCGCACUGAAAGCCACCUGGCUCAUUCUGGCAAAAGUGGGAGCAAUUCCCAUUGGCCAGAGAGCACUCAUCAA
..(((((((((.((.((((....))))..((....((....))....)).........))))))))((((..((((((...((((((((...)))))))).)))))))))).....))). (-41.58 = -41.78 +   0.20)

alignment

secondary structure

dotplot

Window 1

Location	7,540,453 – 7,540,573
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.33
Mean single sequence MFE	-44.70
Consensus MFE	-39.58
Energy contribution	-39.22
Covariance contribution	-0.36
Combinations/Pair	1.14
Mean z-score	-1.65
Structure conservation index	0.89
SVM decision value	1.54
SVM RNA-class probability	0.962211
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7540453 120 + 23771897
UUGCCAGAACGAGCCUGGUGGCUUUCAGUGCGCCUGUCCCUUGGGCUAUGCCCUAUCCGAGGAUAUGCGCACCUGUCAGGACAUUGAUGAGUGCCUCGAUAGCAAUGGCCAAUGCUCGCA
.........(((((....(((((....((((((.((((((..((((...)))).....).))))).))))))((((((((.((((....))))))).)))))....)))))..))))).. ( -47.10)
>DroSec_CAF1 9662 120 + 1
UUGUCAGAAUGAACCAGGUGGCUUUCAGUGCGCCUGUCCCUUGGGCCAUGCUCUAUCCGAGGAUAUGCGCACCUGUCAGGACAUUGACGAGUGCCUCGAUAGCAAUGGCCAAUGCUCGCA
.(((.((.......((((((((.....)).)))))).......((((((...(((((.((((.....)((((.((((((....)))))).))))))))))))..))))))....)).))) ( -39.10)
>DroSim_CAF1 9571 120 + 1
UUGUCAGAAUGAGCCAGGUGGCUUUCAGUGCGCCUGUCCCUUGGGCUAUGCUCUAUCCGAGGAUAUGCGCACCUGUCAGGACAUUGACGAGUGCCUCGAUAGCAAUGGCCAAUGCUCGCA
..........((((....(((((....((((((.(((((.(((((..........)))))))))).))))))((((((((.((((....))))))).)))))....)))))..))))... ( -44.10)
>DroEre_CAF1 9779 120 + 1
UUGCCAGAAUGAGCCAGGUGGCUUCCUGUGCGCCUGUCCUUUGGGAUAUGCCUUAUCAGAGGACAUGCGCACCUGCCAGGACAUUGAUGAGUGCCUCGAUAGCAAUGGCCAGUGCUCGCA
.(((.((..((.((((..((((.....((((((.((((((((((...........)))))))))).))))))..))))((.((((....))))))..........))))))...)).))) ( -45.90)
>DroYak_CAF1 9667 120 + 1
UUGCCAGAAUGAGCCAGGUGGCUUCCAGUGCGCCUGUCCUUUGGGAUAUGCUUUAUCAGAGGAUAUGCGCACCUGUCAGGACAUUGAUGAGUGCAUUGACAGCAAUGGCCAAUGCUCGCA
..........((((....(((((....((((((.((((((((((...........)))))))))).))))))(((((((..((((....))))..)))))))....)))))..))))... ( -47.30)
>consensus
UUGCCAGAAUGAGCCAGGUGGCUUUCAGUGCGCCUGUCCCUUGGGCUAUGCUCUAUCCGAGGAUAUGCGCACCUGUCAGGACAUUGAUGAGUGCCUCGAUAGCAAUGGCCAAUGCUCGCA
.........(((((....(((((....((((((.(((((...(((.....))).......))))).))))))((((((((.((((....))))))).)))))....)))))..))))).. (-39.58 = -39.22 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:39:43 2006