Locus 1302

Sequence ID	2L_DroMel_CAF1
Location	3,436,208 – 3,436,407
Length	199
Max. P	0.610815

overview

Window 5

Location	3,436,208 – 3,436,328
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.84
Mean single sequence MFE	-23.90
Consensus MFE	-15.43
Energy contribution	-15.10
Covariance contribution	-0.33
Combinations/Pair	1.23
Mean z-score	-1.31
Structure conservation index	0.65
SVM decision value	0.16
SVM RNA-class probability	0.610815
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3436208 120 + 22407834
AAAAAAGAAAUAACAUUCAAUGCCAUGCAGACUGAAUGCUCCACUGCAUUUUGUUGCCUGAUAACAAUUCGCUUCGGUUACCUGGCCUUAUUUGUUACUCGUGUGUUUGCACUGGUAAUU
......(((......)))..((((((((((((.((((((......))))))....((.(((((((((...(((..(....)..))).....)))))).))).))))))))).)))))... ( -28.30)
>DroSec_CAF1 25204 90 + 1
A-------------AUUCAAUGCCAUGCAGACUGAAUGCUCCACUGCAUUUUGUUGCCUGAUAACAAUUCGCCUCGGUUACCU-----------------GUGUGUUUGCACUGGUAAUU
.-------------.........((.((((...((((((......))))))..)))).))...............(((((((.-----------------((((....)))).))))))) ( -22.90)
>DroAna_CAF1 30148 100 + 1
A-----------ACUUUCAAUGUCAUGCAGACUGAGUGCCCCAAUGCAUUUGGUUGCCAGAUAAUCAUUUUCAACGGUUACUUUGGUUUAUU---------UGUGUUUUCAGUUGUAAUU
.-----------.....((((.....((((((..(((((......)))))..)))(((((((((((.........))))).)))))).....---------..))).....))))..... ( -21.00)
>DroSim_CAF1 25377 92 + 1
A-----------AUAUUCAAUGCCAAGCAGACUGAAAGCUCCACUGCAUUUUGUUGCCUGAUAACAAUUCGCCUCGGUUACCU-----------------GUGUGUUUGCACUGGUAAUU
.-----------........(((((.((((((....((..((...((...((((((.....))))))...))...))....))-----------------....))))))..)))))... ( -19.00)
>DroEre_CAF1 25716 107 + 1
A-----------ACAUUCAAUGUCAUGCGGACUGAAUGCUCCACUGCAUUUGGUUGUCUGAUAACAAUUUGCCUCGCUUACCUGGCUUUAUUUGUUACU--UGUGUUUGCAUUGGUAAUU
.-----------....((((((.((.((((((..(((((......)))))..)))......((((((...(((..........))).....))))))..--..))).))))))))..... ( -26.80)
>DroYak_CAF1 26831 107 + 1
A-----------ACAUUCAAUGUCAUGCAGACUGAAUGCUCCACUGCAUUUGGUUGCCCGAUAACAAUUUGCCUCGGUUACCUGGCUUUAUUUGUGAUU--UGUGUUUGCACUGGUAAUU
.-----------........(..(((((((((..(((((......)))))..)))((.(((..((((...(((..(....)..))).....))))...)--)).)).)))).))..)... ( -25.40)
>consensus
A___________ACAUUCAAUGCCAUGCAGACUGAAUGCUCCACUGCAUUUGGUUGCCUGAUAACAAUUCGCCUCGGUUACCUGGCUUUAUU_________UGUGUUUGCACUGGUAAUU
....................((((((((((((.((((((......)))))).((.((((((.......)))....))).)).......................))))))).)))))... (-15.43 = -15.10 +  -0.33)

alignment

secondary structure

dotplot

Window 6

Location	3,436,208 – 3,436,328
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.84
Mean single sequence MFE	-22.40
Consensus MFE	-14.52
Energy contribution	-16.27
Covariance contribution	1.75
Combinations/Pair	1.04
Mean z-score	-1.20
Structure conservation index	0.65
SVM decision value	-0.03
SVM RNA-class probability	0.518491
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3436208 120 - 22407834
AAUUACCAGUGCAAACACACGAGUAACAAAUAAGGCCAGGUAACCGAAGCGAAUUGUUAUCAGGCAACAAAAUGCAGUGGAGCAUUCAGUCUGCAUGGCAUUGAAUGUUAUUUCUUUUUU
.....(((.((((.((......))..........(((.((((((...........)))))).))).......)))).)))((((((((((((....)).))))))))))........... ( -28.70)
>DroSec_CAF1 25204 90 - 1
AAUUACCAGUGCAAACACAC-----------------AGGUAACCGAGGCGAAUUGUUAUCAGGCAACAAAAUGCAGUGGAGCAUUCAGUCUGCAUGGCAUUGAAU-------------U
..(((((.(((......)))-----------------.)))))..((..(((..(((((((((((.....(((((......)))))..))))).)))))))))..)-------------) ( -20.60)
>DroAna_CAF1 30148 100 - 1
AAUUACAACUGAAAACACA---------AAUAAACCAAAGUAACCGUUGAAAAUGAUUAUCUGGCAACCAAAUGCAUUGGGGCACUCAGUCUGCAUGACAUUGAAAGU-----------U
......((((.........---------......((((.(((...((((.....(.....)...))))....))).))))........(((.....)))......)))-----------) ( -11.10)
>DroSim_CAF1 25377 92 - 1
AAUUACCAGUGCAAACACAC-----------------AGGUAACCGAGGCGAAUUGUUAUCAGGCAACAAAAUGCAGUGGAGCUUUCAGUCUGCUUGGCAUUGAAUAU-----------U
......((((((.......(-----------------(((((((.(((((..(((((.....(....).....)))))...)))))..)).)))))))))))).....-----------. ( -21.01)
>DroEre_CAF1 25716 107 - 1
AAUUACCAAUGCAAACACA--AGUAACAAAUAAAGCCAGGUAAGCGAGGCAAAUUGUUAUCAGACAACCAAAUGCAGUGGAGCAUUCAGUCCGCAUGACAUUGAAUGU-----------U
.....(((.((((......--.............(((..(....)..)))...(((((....))))).....)))).)))(((((((((((.....)))..)))))))-----------) ( -22.90)
>DroYak_CAF1 26831 107 - 1
AAUUACCAGUGCAAACACA--AAUCACAAAUAAAGCCAGGUAACCGAGGCAAAUUGUUAUCGGGCAACCAAAUGCAGUGGAGCAUUCAGUCUGCAUGACAUUGAAUGU-----------U
.....(((.((((......--.............(((.((...))..)))...........((....))...)))).)))(((((((((((.....)))..)))))))-----------) ( -30.10)
>consensus
AAUUACCAGUGCAAACACA_________AAUAAAGCCAGGUAACCGAGGCAAAUUGUUAUCAGGCAACAAAAUGCAGUGGAGCAUUCAGUCUGCAUGACAUUGAAUGU___________U
.....(((.((((.........................(((((.(((......)))))))).(....)....)))).))).((((((((((.....)))..)))))))............ (-14.52 = -16.27 +   1.75)

alignment

secondary structure

dotplot

Window 7

Location	3,436,288 – 3,436,407
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.33
Mean single sequence MFE	-31.03
Consensus MFE	-21.84
Energy contribution	-22.48
Covariance contribution	0.64
Combinations/Pair	1.19
Mean z-score	-0.99
Structure conservation index	0.70
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3436288 119 + 22407834
CCUGGCCUUAUUUGUUACUCGUGUGUUUGCACUGGUAAUUGCAGCACGCUGCUGCAAACGAUUUGCCGGACAAAAGGCUUAUAAAAAGCCGCAGUCUGAGCCAUCGUCUUCGAACUUCA-
..............(((((.((((....)))).)))))(((((((.....)))))))(((((..(((((((....(((((.....)))))...))))).)).)))))............- ( -37.40)
>DroSec_CAF1 25271 102 + 1
CCU-----------------GUGUGUUUGCACUGGUAAUUGCAGCACGUUGCUGCAACCGAUUUGCCGGACAAAAGGCCUAUGAAAAGCCGCAGUCUGAGCCGCCGACUUCGAACUUCA-
...-----------------....(((((...((((..(((((((.....))))))).......(((((((....(((.........)))...))))).)).))))....)))))....- ( -28.70)
>DroAna_CAF1 30217 108 + 1
CUUUGGUUUAUU---------UGUGUUUUCAGUUGUAAUUGCAGCACGUUGUUGCAACCGAUUUGCCGGACAA-AGGCUUAUGAAAAGCCCCAGCCAACGC-UUCGUCUUU-AACUUCAA
..((((((..((---------(((..............(((((((.....)))))))(((......)))))))-)(((((.....)))))..))))))...-.........-........ ( -24.70)
>DroSim_CAF1 25446 102 + 1
CCU-----------------GUGUGUUUGCACUGGUAAUUGCAGCACGUUGCUGCAACCGAUUUGCCGGACAAAAGACUUAUGAAAAGCCGCAGUCUGAGCCGCCGACUUCGAACUUCA-
((.-----------------((((....)))).))...(((((((.....))))))).(((.(((.(((.....(((((..((......)).)))))...))).)))..))).......- ( -27.80)
>DroEre_CAF1 25785 105 + 1
CCUGGCUUUAUUUGUUACU--UGUGUUUGCAUUGGUAAUUGCAGCGCGUUGCAGCAACCGAUUUGCCGGACAAAAGGCUUAUGAAAAGCCGCAGUCUGAGCCACCAU-------------
..((((((...((((....--..(((((((((((((..((((((....))))))..)))))..)).))))))...(((((.....)))))))))...))))))....------------- ( -33.60)
>DroYak_CAF1 26900 116 + 1
CCUGGCUUUAUUUGUGAUU--UGUGUUUGCACUGGUAAUUGCAGCACGUUGUUGCAACCAAUUUGCCGGACAAAAGGCUUAUGAAAAGCCGCAGUCUGAGCCGCCGUCUUC-AACUUCG-
...(((((...((((..((--((((....).((((((((((((((.....))))))).....)))))))))))).(((((.....)))))))))...))))).........-.......- ( -34.00)
>consensus
CCUGGCUUUAUU_________UGUGUUUGCACUGGUAAUUGCAGCACGUUGCUGCAACCGAUUUGCCGGACAAAAGGCUUAUGAAAAGCCGCAGUCUGAGCCGCCGUCUUC_AACUUCA_
......................(((....)))((((..(((((((.....))))))).......(((((((....(((((.....)))))...))))).)).)))).............. (-21.84 = -22.48 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:12 2006