Locus 4292

Sequence ID	3R_DroMel_CAF1
Location	11,415,892 – 11,416,080
Length	188
Max. P	0.996066

overview

Window 3

Location	11,415,892 – 11,416,011
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.49
Mean single sequence MFE	-42.10
Consensus MFE	-39.92
Energy contribution	-40.36
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.22
Structure conservation index	0.95
SVM decision value	0.32
SVM RNA-class probability	0.688421
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11415892 119 + 27905053
CCACCCAGUCAUUACCAUCAAUUUCCAGCCCCAAGGGCAGUGGACAA-GUUCGGGUUUUGGCACAUGGGUCAUUUGUGUGCAUUUGUUUUCAGGGUGUCCCCGGCAGGAUCCUGCUGGCC
.(((((...((..(((...((((((((((((...))))..))))..)-)))..)))..))(((((..(.....)..)))))...........)))))...(((((((....))))))).. ( -44.10)
>DroSec_CAF1 163534 119 + 1
CCACCCAGUCAUUACCAUCAAUUUCCAGCCCCAAGGGCAGUGGACAA-GUUCGGGUUUUGGCACAUGGGUCAUUUGUGUGCAUUUGUUUUCAGGGUGUCCCCGGCAGGAUCCUGCUGGCC
.(((((...((..(((...((((((((((((...))))..))))..)-)))..)))..))(((((..(.....)..)))))...........)))))...(((((((....))))))).. ( -44.10)
>DroSim_CAF1 156320 119 + 1
CCACCCAGUCAUUACCAUCAAUUUCCAGCCCCAAGGGCAGUGGACAA-GUUCGGGUUUUGGCACAUGGGUCAUUUGUGUGCAUUUGUUUUCAGGGUUUCCCCGGCAGGAUCCUGCUGGCC
..((((...((..(((...((((((((((((...))))..))))..)-)))..)))..))(((((..(.....)..)))))...........))))....(((((((....))))))).. ( -41.00)
>DroEre_CAF1 151324 120 + 1
CCAGCCAGUCAUUACCAUCAAUUUGCAGCCCCAAGGGCAGCGGACCAGGUUCGGGUUUUGGCACAUGGGUCAUUUGUGUGCAUUUGUUUUCAGGGUGUCCCCGGCAGGAUCCUGCUGGCC
...((((((....(((.....(((((.((((...)))).)))))...)))..(((((((((((((..(.....)..)))))...........(((....)))..)))))))).)))))). ( -42.10)
>DroYak_CAF1 155501 120 + 1
CCACCCAGUCAUUACCAUCAAUUUCCAGCCCCAAGGGCAGUGGACAAGGUUCGGGUUUUGGCACAUGGGUCAUUUGUGUGCAUUUGUUUUCAGGGUGUCCCCGGCUGGAUCCUGCUGGCC
.(((((...((..(((..(....((((((((...))))..))))....)....)))..))(((((..(.....)..)))))...........)))))...(((((.(....).))))).. ( -39.20)
>consensus
CCACCCAGUCAUUACCAUCAAUUUCCAGCCCCAAGGGCAGUGGACAA_GUUCGGGUUUUGGCACAUGGGUCAUUUGUGUGCAUUUGUUUUCAGGGUGUCCCCGGCAGGAUCCUGCUGGCC
.(((((...((..(((...........((((...))))..(((((...))))))))..))(((((..(.....)..)))))...........)))))...(((((((....))))))).. (-39.92 = -40.36 +   0.44)

alignment

secondary structure

dotplot

Window 4

Location	11,415,932 – 11,416,046
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.40
Mean single sequence MFE	-35.37
Consensus MFE	-32.30
Energy contribution	-32.30
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.01
Structure conservation index	0.91
SVM decision value	2.65
SVM RNA-class probability	0.996066
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11415932 114 - 27905053
AAUCAAC-----GGCUGCCGGGCAGGAUAAGCAAUGUCCUGGCCAGCAGGAUCCUGCCGGGGACACCCUGAAAACAAAUGCACACAAAUGACCCAUGUGCCAAAACCCGAAC-UUGUCCA
......(-----(((.((.((.(((((((.....))))))).)).))((....)))))).(((((..............(((((...........)))))............-.))))). ( -34.73)
>DroSec_CAF1 163574 114 - 1
AAUCAAC-----GGCUGCCGGGCAGGAUAAGCAAUGUCCUGGCCAGCAGGAUCCUGCCGGGGACACCCUGAAAACAAAUGCACACAAAUGACCCAUGUGCCAAAACCCGAAC-UUGUCCA
......(-----(((.((.((.(((((((.....))))))).)).))((....)))))).(((((..............(((((...........)))))............-.))))). ( -34.73)
>DroSim_CAF1 156360 114 - 1
AAUCAAC-----GGCUGCCGGGCAGGAUAAGCAAUGUCCUGGCCAGCAGGAUCCUGCCGGGGAAACCCUGAAAACAAAUGCACACAAAUGACCCAUGUGCCAAAACCCGAAC-UUGUCCA
......(-----((((((.((.(((((((.....))))))).)).)))).........(((....)))...........(((((...........)))))......)))...-....... ( -36.10)
>DroEre_CAF1 151364 120 - 1
AAUCAACGCAUCGGCUGCCGGGCAGGAUAAGCAAUGUCCUGGCCAGCAGGAUCCUGCCGGGGACACCCUGAAAACAAAUGCACACAAAUGACCCAUGUGCCAAAACCCGAACCUGGUCCG
..........((((((((.((.(((((((.....))))))).)).))))........(((((...))))).........(((((...........)))))......)))).......... ( -35.40)
>DroYak_CAF1 155541 115 - 1
AAUCAAC-----GGCUGCCGGGCAGGAUAAGCAAUGUCCUGGCCAGCAGGAUCCAGCCGGGGACACCCUGAAAACAAAUGCACACAAAUGACCCAUGUGCCAAAACCCGAACCUUGUCCA
......(-----((((((.((.(((((((.....))))))).)).)).(....)))))).(((((..............(((((...........)))))..............))))). ( -35.89)
>consensus
AAUCAAC_____GGCUGCCGGGCAGGAUAAGCAAUGUCCUGGCCAGCAGGAUCCUGCCGGGGACACCCUGAAAACAAAUGCACACAAAUGACCCAUGUGCCAAAACCCGAAC_UUGUCCA
..(((.......((((((.((.(((((((.....))))))).)).)))(....).)))(((....))))))........(((((...........))))).................... (-32.30 = -32.30 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	11,415,971 – 11,416,080
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.47
Mean single sequence MFE	-34.62
Consensus MFE	-29.70
Energy contribution	-29.58
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-1.73
Structure conservation index	0.86
SVM decision value	1.46
SVM RNA-class probability	0.955897
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11415971 109 + 27905053
CAUUUGUUUUCAGGGUGUCCCCGGCAGGAUCCUGCUGGCCAGGACAUUGCUUAUCCUGCCCGGCAGCC-----GUUGAUUUUUCCCAGCUUCCUCCGCAGCUCGC------AAUACACUC
............((((((....((.((((..(((((((.(((((.(.....).))))).)))))))..-----((((........)))).))))))((.....))------...)))))) ( -35.20)
>DroSec_CAF1 163613 109 + 1
CAUUUGUUUUCAGGGUGUCCCCGGCAGGAUCCUGCUGGCCAGGACAUUGCUUAUCCUGCCCGGCAGCC-----GUUGAUUUUUCCCAGCUUCCUCUGCAGCUCGC------CAUACACUC
.............((((....(((.((((..(((((((.(((((.(.....).))))).)))))))..-----((((........)))).))))))).....)))------)........ ( -33.30)
>DroSim_CAF1 156399 109 + 1
CAUUUGUUUUCAGGGUUUCCCCGGCAGGAUCCUGCUGGCCAGGACAUUGCUUAUCCUGCCCGGCAGCC-----GUUGAUUUUUCCCAGCUUCCUCUGCAGCUUGC------CAUACACUC
............(((....)))((((((...(((((((.(((((.(.....).))))).)))))))..-----((((........))))...........)))))------)........ ( -35.10)
>DroEre_CAF1 151404 119 + 1
CAUUUGUUUUCAGGGUGUCCCCGGCAGGAUCCUGCUGGCCAGGACAUUGCUUAUCCUGCCCGGCAGCCGAUGCGUUGAUUUUUC-CAGCUUCCUCUGCAGCUCGCAGUACUCGUACACUC
............(((((((((((((((....)))))))...))))..........((((...((((..((.((...((....))-..)).))..)))).....)))).))))........ ( -35.50)
>DroYak_CAF1 155581 108 + 1
CAUUUGUUUUCAGGGUGUCCCCGGCUGGAUCCUGCUGGCCAGGACAUUGCUUAUCCUGCCCGGCAGCC-----GUUGAUUUUUC-CAGCUUCCUCUGCAGCUCGC------CAUACACUC
............((((((...((((((....(((((((.(((((.(.....).))))).)))))))..-----((((.......-))))........)))).)).------...)))))) ( -34.00)
>consensus
CAUUUGUUUUCAGGGUGUCCCCGGCAGGAUCCUGCUGGCCAGGACAUUGCUUAUCCUGCCCGGCAGCC_____GUUGAUUUUUCCCAGCUUCCUCUGCAGCUCGC______CAUACACUC
............((((.....(((.((((..(((((((.(((((.(.....).))))).))))))).......((((........)))).)))))))..))))................. (-29.70 = -29.58 +  -0.12)

alignment

secondary structure

dotplot

Window 6

Location	11,415,971 – 11,416,080
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.47
Mean single sequence MFE	-39.90
Consensus MFE	-32.92
Energy contribution	-32.92
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.26
Structure conservation index	0.83
SVM decision value	2.05
SVM RNA-class probability	0.986795
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11415971 109 - 27905053
GAGUGUAUU------GCGAGCUGCGGAGGAAGCUGGGAAAAAUCAAC-----GGCUGCCGGGCAGGAUAAGCAAUGUCCUGGCCAGCAGGAUCCUGCCGGGGACACCCUGAAAACAAAUG
...(((...------((((.((((...((.(((((...........)-----)))).))((.(((((((.....))))))).)).))))..))..))(((((...)))))...))).... ( -36.90)
>DroSec_CAF1 163613 109 - 1
GAGUGUAUG------GCGAGCUGCAGAGGAAGCUGGGAAAAAUCAAC-----GGCUGCCGGGCAGGAUAAGCAAUGUCCUGGCCAGCAGGAUCCUGCCGGGGACACCCUGAAAACAAAUG
...(((..(------((((.((((...((.(((((...........)-----)))).))((.(((((((.....))))))).)).))))..))..)))(((....))).....))).... ( -40.20)
>DroSim_CAF1 156399 109 - 1
GAGUGUAUG------GCAAGCUGCAGAGGAAGCUGGGAAAAAUCAAC-----GGCUGCCGGGCAGGAUAAGCAAUGUCCUGGCCAGCAGGAUCCUGCCGGGGAAACCCUGAAAACAAAUG
...(((..(------(((.(((((...((.(((((...........)-----)))).))((.(((((((.....))))))).)).))))...).))))(((....))).....))).... ( -43.00)
>DroEre_CAF1 151404 119 - 1
GAGUGUACGAGUACUGCGAGCUGCAGAGGAAGCUG-GAAAAAUCAACGCAUCGGCUGCCGGGCAGGAUAAGCAAUGUCCUGGCCAGCAGGAUCCUGCCGGGGACACCCUGAAAACAAAUG
....(((.((...((((.....((((..((.((..-((....))...)).))..)))).((.(((((((.....))))))).)).))))..)).)))(((((...))))).......... ( -39.10)
>DroYak_CAF1 155581 108 - 1
GAGUGUAUG------GCGAGCUGCAGAGGAAGCUG-GAAAAAUCAAC-----GGCUGCCGGGCAGGAUAAGCAAUGUCCUGGCCAGCAGGAUCCAGCCGGGGACACCCUGAAAACAAAUG
...(((..(------((((.((((...((.(((((-..........)-----)))).))((.(((((((.....))))))).)).))))..))..)))(((....))).....))).... ( -40.30)
>consensus
GAGUGUAUG______GCGAGCUGCAGAGGAAGCUGGGAAAAAUCAAC_____GGCUGCCGGGCAGGAUAAGCAAUGUCCUGGCCAGCAGGAUCCUGCCGGGGACACCCUGAAAACAAAUG
...(((.........((.((((........))))....................((((.((.(((((((.....))))))).)).))))......))(((((...)))))...))).... (-32.92 = -32.92 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:57 2006