Locus 9284

Sequence ID	3R_DroMel_CAF1
Location	24,748,227 – 24,748,322
Length	95
Max. P	0.564224

overview

Window 4

Location	24,748,227 – 24,748,322
Length	95
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.22
Mean single sequence MFE	-19.40
Consensus MFE	-13.98
Energy contribution	-13.57
Covariance contribution	-0.41
Combinations/Pair	1.29
Mean z-score	-1.43
Structure conservation index	0.72
SVM decision value	0.06
SVM RNA-class probability	0.564224
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24748227 95 + 27905053
---UU-UUCAAAUGUGUAGAACCGUU--GCCGGCCUGUUUUGUUCGUUUUCGUU-UACAACCGAAUAUCGAAAGAUCAACC--CAUUUACACAUU----GCUACACAC------------
---..-....((((((((((...(((--(.(((..(((......((....))..-.))).)))...(((....))))))).--..))))))))))----.........------------ ( -19.60)
>DroSec_CAF1 2283 95 + 1
---UU-UUGAAAUGUGUAGAGCCGUU--GCCGGCCUGUUUUGUUCGUUUUCGUU-UACAACCGAAUAUCGAAAGAUCAACC--CAUUUACACAUU----GCUACACAC------------
---..-....((((((((((((((..--..)))).((.....((((..((((..-......))))...))))....))...--..))))))))))----.........------------ ( -21.70)
>DroSim_CAF1 2282 94 + 1
---UU-UUCAAAUGUGUAAAGCCGUU--GCCGGCCUGUUUUGUUCGUUUUCGUU-UACAACCGAAUAUCGAAAGAUCAACC--CAUUUACACA-U----GCUACACAC------------
---..-.....(((((((((((((..--..)))).((.....((((..((((..-......))))...))))....))...--..))))))))-)----.........------------ ( -20.70)
>DroEre_CAF1 2271 98 + 1
---UUUUUCAAAUGUGUAGAACUGUC--GCCGGCCUGUUUUGUUCGUUUUCGUU-UACAACCGAAUAUCGAAAGAUCAACC--CAUUUACACAUU----GCUACACAC----------AC
---.........(((((((...(((.--...((..((.....((((..((((..-......))))...))))....))..)--)......)))..----.))))))).----------.. ( -17.90)
>DroYak_CAF1 2276 107 + 1
---UU-UUCAAAUGUGUAGAACUGUC--GCCGGCCUGUUUUGUUCGUUUUCGUU-UACAACCGAAUAUCGAAAGAUCAACC--CAUUCACACAUU----GCUACACACACACAAACACAC
---..-......(((((((...(((.--...((..((.....((((..((((..-......))))...))))....))..)--)......)))..----.)))))))............. ( -17.90)
>DroPer_CAF1 2457 104 + 1
AUGUU-UUCAGAUGUGUAGAAUUAUCGCGCCAAUCCGUUUUGUUCGUUUUCGUUCUAUUGUCGAAUAUCGAAAACUCAACACACAUUUAUCCAUUACAUGCUAUA---------------
((((.-...((((((((.((((....(((......)))...))))(((((((...((((....)))).))))))).....)))))))).......))))......--------------- ( -18.60)
>consensus
___UU_UUCAAAUGUGUAGAACCGUC__GCCGGCCUGUUUUGUUCGUUUUCGUU_UACAACCGAAUAUCGAAAGAUCAACC__CAUUUACACAUU____GCUACACAC____________
..........((((((((((.(((......))).........((((..((((.........))))...)))).............))))))))))......................... (-13.98 = -13.57 +  -0.41)

alignment

secondary structure

dotplot

Window 5

Location	24,748,227 – 24,748,322
Length	95
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.22
Mean single sequence MFE	-23.90
Consensus MFE	-15.98
Energy contribution	-15.90
Covariance contribution	-0.08
Combinations/Pair	1.25
Mean z-score	-1.45
Structure conservation index	0.67
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24748227 95 - 27905053
------------GUGUGUAGC----AAUGUGUAAAUG--GGUUGAUCUUUCGAUAUUCGGUUGUA-AACGAAAACGAACAAAACAGGCCGGC--AACGGUUCUACACAUUUGAA-AA---
------------((((((((.----..........((--..(((....((((...((((......-..))))..)))))))..))(((((..--..))))))))))))).....-..--- ( -24.70)
>DroSec_CAF1 2283 95 - 1
------------GUGUGUAGC----AAUGUGUAAAUG--GGUUGAUCUUUCGAUAUUCGGUUGUA-AACGAAAACGAACAAAACAGGCCGGC--AACGGCUCUACACAUUUCAA-AA---
------------((((((((.----..........((--..(((....((((...((((......-..))))..)))))))..))(((((..--..))))))))))))).....-..--- ( -27.20)
>DroSim_CAF1 2282 94 - 1
------------GUGUGUAGC----A-UGUGUAAAUG--GGUUGAUCUUUCGAUAUUCGGUUGUA-AACGAAAACGAACAAAACAGGCCGGC--AACGGCUUUACACAUUUGAA-AA---
------------.........----(-(((((((.((--..(((....((((...((((......-..))))..)))))))..))(((((..--..))))))))))))).....-..--- ( -26.00)
>DroEre_CAF1 2271 98 - 1
GU----------GUGUGUAGC----AAUGUGUAAAUG--GGUUGAUCUUUCGAUAUUCGGUUGUA-AACGAAAACGAACAAAACAGGCCGGC--GACAGUUCUACACAUUUGAAAAA---
..----------((((((((.----(((.(((...((--(.(((....((((...((((......-..))))..)))).....))).)))..--.))))))))))))))........--- ( -24.00)
>DroYak_CAF1 2276 107 - 1
GUGUGUUUGUGUGUGUGUAGC----AAUGUGUGAAUG--GGUUGAUCUUUCGAUAUUCGGUUGUA-AACGAAAACGAACAAAACAGGCCGGC--GACAGUUCUACACAUUUGAA-AA---
............((((((((.----(((.(((...((--(.(((....((((...((((......-..))))..)))).....))).)))..--.)))))))))))))).....-..--- ( -22.90)
>DroPer_CAF1 2457 104 - 1
---------------UAUAGCAUGUAAUGGAUAAAUGUGUGUUGAGUUUUCGAUAUUCGACAAUAGAACGAAAACGAACAAAACGGAUUGGCGCGAUAAUUCUACACAUCUGAA-AACAU
---------------..(((.((((..((((......(((((..((((((((...(((.......))))))))))...(.....)..)..))))).....)))).)))))))..-..... ( -18.60)
>consensus
____________GUGUGUAGC____AAUGUGUAAAUG__GGUUGAUCUUUCGAUAUUCGGUUGUA_AACGAAAACGAACAAAACAGGCCGGC__AACAGUUCUACACAUUUGAA_AA___
............((((((((....................(((.....((((...((((.........))))..))))...))).(((((......)))))))))))))........... (-15.98 = -15.90 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:30:42 2006