Locus 55

Sequence ID	2L_DroMel_CAF1
Location	216,786 – 216,918
Length	132
Max. P	0.996216

overview

Window 8

Location	216,786 – 216,905
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.09
Mean single sequence MFE	-49.70
Consensus MFE	-25.07
Energy contribution	-25.27
Covariance contribution	0.20
Combinations/Pair	1.20
Mean z-score	-1.73
Structure conservation index	0.50
SVM decision value	-0.00
SVM RNA-class probability	0.532312
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 216786 119 + 22407834
GACAUUCCGGGAAGCAGAGACGAUAGGGAGGUGGCAUUUCCACCUGCUGCAGCUGCCGCAACGGCCGCUGCCACAGCAGCAUUGAUGCUUUUAGCAUCCAAGCCAGGUAAACU-GUUGGA
.....(((((...((..........((.((((((.....)))))).))(((((.((((...)))).)))))....)).((...(((((.....)))))...))(((.....))-)))))) ( -41.10)
>DroVir_CAF1 11967 119 + 1
GACAUGCCCGGCAGCAAUGCCGACAAGGAUGUGGCAUUGCCGCCGCUUGCCGCAGCGGCGACCGCAGCCGCGACAGCUGCAUUGAUGCUAUUCGCAUCCAGGCCCGGCAGCGUGGUGG-G
........((((.((((((((.(((....))))))))))).))))((..((((.(((((.......)))))....(((((.(((((((.....)))).))).....)))))))))..)-) ( -58.60)
>DroGri_CAF1 10362 119 + 1
GACAUGCCCGGCAGCAGGGCAGAGAGCGAGGUGGCAUUGCCACCACUAGCGGCAGCCGCAACAGCAGCUGCCACUGCUGCAUUUAUGCUAUUCGCAUCCAGGCCAGGCAGCGUUGUUG-U
(((.((((.(((((((((((((...((..((((((...))))))....((((...))))....))..))))).)))))......((((.....))))....))).))))..)))....-. ( -52.60)
>DroWil_CAF1 10817 117 + 1
GACAUGCCCGGCAGGAGGGAUGAUAGCGAUGUGGCAUUGCCACCAGCUGCAGCAGCUGCCACAGCAGCAGCAACUGCCGCAUUGAUGCUAUUGGCAUCGAGUCCUGGUAA--U-GUUGGU
((((((((((((((......((.((((...(((((...)))))..))))))((.(((((....))))).))..))))))..(((((((.....))))))).....))).)--)-)))... ( -48.40)
>DroMoj_CAF1 9755 119 + 1
GACAUGCCCGGCAGCAGAGCUGACAGAGAUGUGGCAUUGCCGCCACUGGCUGCCGCUGCGACAGCAGCUGCCACAGCCGCAUUGAUGCUGUUCGCAUCCAAACCAGGCAGCGUUGUUG-G
.......((((((((.((((.(.((..((((((((...((((....)))).((.(((((....))))).))....))))))))..))).))))((..((......))..)))))))))-) ( -49.50)
>DroAna_CAF1 12042 116 + 1
GACAUGCCAGGCAGCAGGCUGGACAGCGAGGUGGCAUUACCACCUGCCGCAGCUGCCGCCACAGCAGCCGCCACCGCAGCAUUGAUGUUGUUCGCAUCCAGUAGCGGUAGAGU----GGA
....(((..(((.((((.(((....((.((((((.....))))))))..))))))).)))...))).((((((((((.((...(((((.....)))))..)).))))).).))----)). ( -48.00)
>consensus
GACAUGCCCGGCAGCAGGGCCGACAGCGAGGUGGCAUUGCCACCACCUGCAGCAGCCGCAACAGCAGCUGCCACAGCAGCAUUGAUGCUAUUCGCAUCCAGGCCAGGCAGCGU_GUUG_A
....((((..((.((...............((((.....)))).....((.((.((((...)))).)).))....)).))...(((((.....))))).......))))........... (-25.07 = -25.27 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	216,786 – 216,905
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.09
Mean single sequence MFE	-55.53
Consensus MFE	-34.13
Energy contribution	-34.24
Covariance contribution	0.11
Combinations/Pair	1.29
Mean z-score	-3.32
Structure conservation index	0.61
SVM decision value	2.67
SVM RNA-class probability	0.996216
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 216786 119 - 22407834
UCCAAC-AGUUUACCUGGCUUGGAUGCUAAAAGCAUCAAUGCUGCUGUGGCAGCGGCCGUUGCGGCAGCUGCAGCAGGUGGAAAUGCCACCUCCCUAUCGUCUCUGCUUCCCGGAAUGUC
(((.((-(((......(((...(((((.....)))))...))))))))(((((.(((.(((((((...)))))))((((((.....)))))).......))).)))))....)))..... ( -44.80)
>DroVir_CAF1 11967 119 - 1
C-CCACCACGCUGCCGGGCCUGGAUGCGAAUAGCAUCAAUGCAGCUGUCGCGGCUGCGGUCGCCGCUGCGGCAAGCGGCGGCAAUGCCACAUCCUUGUCGGCAUUGCUGCCGGGCAUGUC
(-((.....((((((.((((..(((((.....)))))...(((((((...)))))))))))((....))))).)))(((((((((((((((....))).)))))))))))))))...... ( -65.20)
>DroGri_CAF1 10362 119 - 1
A-CAACAACGCUGCCUGGCCUGGAUGCGAAUAGCAUAAAUGCAGCAGUGGCAGCUGCUGUUGCGGCUGCCGCUAGUGGUGGCAAUGCCACCUCGCUCUCUGCCCUGCUGCCGGGCAUGUC
.-.....(((.((((((((..((((((.....))))....((((.((((((((((((....)))))))))))).(.((((((...)))))).).....))))))....))))))))))). ( -60.90)
>DroWil_CAF1 10817 117 - 1
ACCAAC-A--UUACCAGGACUCGAUGCCAAUAGCAUCAAUGCGGCAGUUGCUGCUGCUGUGGCAGCUGCUGCAGCUGGUGGCAAUGCCACAUCGCUAUCAUCCCUCCUGCCGGGCAUGUC
....((-(--(..((((((...((((...(((((..((.((((((((((((..(....)..))))))))))))..))(((((...)))))...)))))))))..))))...))..)))). ( -50.20)
>DroMoj_CAF1 9755 119 - 1
C-CAACAACGCUGCCUGGUUUGGAUGCGAACAGCAUCAAUGCGGCUGUGGCAGCUGCUGUCGCAGCGGCAGCCAGUGGCGGCAAUGCCACAUCUCUGUCAGCUCUGCUGCCGGGCAUGUC
.-.....(((.((((((((...(((((.....)))))...(((((((((((.(((((((...))))))).))))((((((....))))))........)))))..)).))))))))))). ( -55.40)
>DroAna_CAF1 12042 116 - 1
UCC----ACUCUACCGCUACUGGAUGCGAACAACAUCAAUGCUGCGGUGGCGGCUGCUGUGGCGGCAGCUGCGGCAGGUGGUAAUGCCACCUCGCUGUCCAGCCUGCUGCCUGGCAUGUC
...----...(((((((..(..((((.......))))...)..))))))).((((((((.(((((((((((((((((((((.....)))))).))))..))).))))))))))))).))) ( -56.70)
>consensus
A_CAAC_ACGCUACCUGGCCUGGAUGCGAAUAGCAUCAAUGCAGCUGUGGCAGCUGCUGUCGCGGCUGCUGCAACUGGUGGCAAUGCCACAUCGCUGUCAGCCCUGCUGCCGGGCAUGUC
.........((((((.......(((((.....)))))...((.(((((.(((((....))))).))))).))....)))))).(((((........................)))))... (-34.13 = -34.24 +   0.11)

alignment

secondary structure

dotplot

Window 0

Location	216,826 – 216,918
Length	92
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	76.56
Mean single sequence MFE	-35.48
Consensus MFE	-20.67
Energy contribution	-21.58
Covariance contribution	0.92
Combinations/Pair	1.16
Mean z-score	-1.98
Structure conservation index	0.58
SVM decision value	1.11
SVM RNA-class probability	0.916051
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 216826 92 + 22407834
CACCUGCUGCAGCUGCCGCAACGGCCGCUGCCACAGCAGCAUUGAUGCUUUUAGCAUCCAAGCCAGGUAAACU-GUUGGAAGAA---GAGGGCUUU
...((((((((((.((((...)))).)))))...))))).......((((((..(.(((((..(((.....))-)))))).)..---))))))... ( -34.40)
>DroSim_CAF1 9116 92 + 1
CACCUGCCGCAGCUGCCGCAACGGCCGCUGCCACAGCAGCAUUAAUGCUUUUGGCAUCCAAGCCAGGCAAACU-GUUGGAAGAA---GAGGGCUUU
.....((((((((.((((...)))).)))))..((((((......((((..((((......))))))))..))-))))......---...)))... ( -35.00)
>DroEre_CAF1 9407 92 + 1
CACCUGCUGCAGCUGCCGCAACGGCUGCUGCCACCGCAGCAUUGAUGCUUUUGGCAUCCAAUCCAGGUAAGCU-GUUGGAAGAA---GACGGCUUU
.(((((..(((((.((((...)))).)))))............(((((.....))))).....)))))(((((-(((.......---)))))))). ( -35.20)
>DroYak_CAF1 11169 92 + 1
CACCUGCUGCAGCUGCCGCAACGGCCGCUGCCACCGCAGCAUUGAUGCUUUUGGCAUCCAAGCCAGGUAAGCU-GUUGGAAGAG---GAGGGUUUU
..(((.(((((((.((((...)))).)))))..(((((((.....((((..((((......)))))))).)))-).)))...))---.)))..... ( -35.70)
>DroMoj_CAF1 9795 86 + 1
CGCCACUGGCUGCCGCUGCGACAGCAGCUGCCACAGCCGCAUUGAUGCUGUUCGCAUCCAAACCAGGCAGCGUUGUUG-GCGCUGUU---------
((((((..(((((((((((....)))))(((.(((((.........)))))..))).........))))))...).))-))).....--------- ( -36.30)
>DroAna_CAF1 12082 92 + 1
CACCUGCCGCAGCUGCCGCCACAGCAGCCGCCACCGCAGCAUUGAUGUUGUUCGCAUCCAGUAGCGGUAGAGU----GGAAGCACUCACGGGCUUG
.....(((((.(((((.......))))).)).(((((.((...(((((.....)))))..)).))))).((((----(....)))))...)))... ( -36.30)
>consensus
CACCUGCUGCAGCUGCCGCAACGGCCGCUGCCACAGCAGCAUUGAUGCUUUUGGCAUCCAAGCCAGGUAAACU_GUUGGAAGAA___GAGGGCUUU
.(((((..(((((.((((...)))).)))))............(((((.....))))).....)))))............................ (-20.67 = -21.58 +   0.92)

alignment

secondary structure

dotplot

Window 1

Location	216,826 – 216,918
Length	92
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	76.56
Mean single sequence MFE	-37.18
Consensus MFE	-27.66
Energy contribution	-27.42
Covariance contribution	-0.25
Combinations/Pair	1.36
Mean z-score	-2.09
Structure conservation index	0.74
SVM decision value	1.79
SVM RNA-class probability	0.977232
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 216826 92 - 22407834
AAAGCCCUC---UUCUUCCAAC-AGUUUACCUGGCUUGGAUGCUAAAAGCAUCAAUGCUGCUGUGGCAGCGGCCGUUGCGGCAGCUGCAGCAGGUG
.........---..........-....((((((.....(((((.....)))))..(((.(((((.(((((....))))).))))).))).)))))) ( -35.90)
>DroSim_CAF1 9116 92 - 1
AAAGCCCUC---UUCUUCCAAC-AGUUUGCCUGGCUUGGAUGCCAAAAGCAUUAAUGCUGCUGUGGCAGCGGCCGUUGCGGCAGCUGCGGCAGGUG
...(((...---....((((.(-((.....)))...))))((((...((((....))))(((((.(((((....))))).)))))...))))))). ( -35.00)
>DroEre_CAF1 9407 92 - 1
AAAGCCGUC---UUCUUCCAAC-AGCUUACCUGGAUUGGAUGCCAAAAGCAUCAAUGCUGCGGUGGCAGCAGCCGUUGCGGCAGCUGCAGCAGGUG
.((((.((.---........))-.))))(((((.....(((((.....)))))..((((((..((((....))))..)))))).......))))). ( -34.20)
>DroYak_CAF1 11169 92 - 1
AAAACCCUC---CUCUUCCAAC-AGCUUACCUGGCUUGGAUGCCAAAAGCAUCAAUGCUGCGGUGGCAGCGGCCGUUGCGGCAGCUGCAGCAGGUG
...(((...---..........-.((((...((((......)))).)))).....(((((((((.(((((....)))))....)))))))))))). ( -33.80)
>DroMoj_CAF1 9795 86 - 1
---------AACAGCGC-CAACAACGCUGCCUGGUUUGGAUGCGAACAGCAUCAAUGCGGCUGUGGCAGCUGCUGUCGCAGCGGCAGCCAGUGGCG
---------.....(((-((.....((((((..((...(((((.....)))))...)).((((((((((...))))))))))))))))...))))) ( -44.30)
>DroAna_CAF1 12082 92 - 1
CAAGCCCGUGAGUGCUUCC----ACUCUACCGCUACUGGAUGCGAACAACAUCAAUGCUGCGGUGGCGGCUGCUGUGGCGGCAGCUGCGGCAGGUG
...(((...(((((....)----))))((((((..(..((((.......))))...)..))))))((((((((((...)))))))))))))..... ( -39.90)
>consensus
AAAGCCCUC___UUCUUCCAAC_AGUUUACCUGGCUUGGAUGCCAAAAGCAUCAAUGCUGCGGUGGCAGCGGCCGUUGCGGCAGCUGCAGCAGGUG
............................(((.......(((((.....)))))..(((((((((.((.(((.....))).)).)))))))))))). (-27.66 = -27.42 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:24:28 2006