Locus 2475

Sequence ID	X_DroMel_CAF1
Location	6,591,956 – 6,592,141
Length	185
Max. P	0.962334

overview

Window 5

Location	6,591,956 – 6,592,064
Length	108
Sequences	3
Columns	108
Reading direction	reverse
Mean pairwise identity	90.51
Mean single sequence MFE	-27.80
Consensus MFE	-24.41
Energy contribution	-24.85
Covariance contribution	0.45
Combinations/Pair	1.03
Mean z-score	-2.36
Structure conservation index	0.88
SVM decision value	0.94
SVM RNA-class probability	0.885467
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6591956 108 - 22224390
UGAUCAUGAUCAUCAUGAUCACGCUACCCUUGAUCCCGCCUCGUUUUUUUUUUUUUUGUGAUUUGUUUACGCUGUUCUCUCGAGAUUUAGCGAAAACAACAAGCGAUU
((((((((.....))))))))((((...........(((..................)))..((((((.(((((.(((....)))..))))).))))))..))))... ( -26.57)
>DroSec_CAF1 7636 100 - 1
UGAUCAUGAUCAUCAUGAUCAGGCUGCCCUUGAUCCCGCCUCGGUU--------UUUGUGAUUUGUUUACCCUGUUCUCUCGAGAUUCAGCGAAAACAACAAGCGAAU
((((((((.....))))))))(((.............)))......--------(((((...((((((.(.(((.(((....)))..))).).))))))...))))). ( -24.62)
>DroSim_CAF1 4444 100 - 1
UGAUCAUGAUCAUCAUGAUCAGGCUGCCCUUGAUCCCGCCUCGGUU--------UUUGUGAUUUGUUUACGCUGUUCUCUCGAGAGUCAGCGAAAACAACAAGCGAAU
((((((((.....))))))))(((.............)))......--------(((((...((((((.(((((((((....)))).))))).))))))...))))). ( -32.22)
>consensus
UGAUCAUGAUCAUCAUGAUCAGGCUGCCCUUGAUCCCGCCUCGGUU________UUUGUGAUUUGUUUACGCUGUUCUCUCGAGAUUCAGCGAAAACAACAAGCGAAU
((((((((.....))))))))(((.............)))...............((((...((((((.(((((.(((....)))..))))).))))))...)))).. (-24.41 = -24.85 +   0.45)

alignment

secondary structure

dotplot

Window 6

Location	6,591,984 – 6,592,101
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.27
Mean single sequence MFE	-29.24
Consensus MFE	-18.46
Energy contribution	-19.14
Covariance contribution	0.68
Combinations/Pair	1.24
Mean z-score	-1.61
Structure conservation index	0.63
SVM decision value	-0.02
SVM RNA-class probability	0.523672
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6591984 117 + 22224390
AGAGAACAGCGUAAACAAAUCACAAAAAAAAAAAAAACGAGGCGGGAUCAAGGGUAGCGUGAUCAUGAUGAUCAUGAUCAUCAAGCAUGCAGCUCAAGAUGAUCAGCCGAAUGGCCG---
........................................(((..(((((.((((.(((((....(((((((....)))))))..))))).))))....))))).))).........--- ( -29.70)
>DroSec_CAF1 7664 109 + 1
AGAGAACAGGGUAAACAAAUCACAAA--------AACCGAGGCGGGAUCAAGGGCAGCCUGAUCAUGAUGAUCAUGAUCACCAGGCAUGCAGCUCAAGAUGAUCCGCCGAAUGGCCG---
.........(((.......((.....--------....))(((((.((((((.((((((((((((((.....)))))))...)))).)))..)).....))))))))).....))).--- ( -33.00)
>DroSim_CAF1 4472 109 + 1
AGAGAACAGCGUAAACAAAUCACAAA--------AACCGAGGCGGGAUCAAGGGCAGCCUGAUCAUGAUGAUCAUGAUCACCAGGCAUGCAGCUCAAGAUGAUCAGCCGAAUGGCCG---
..........................--------..(((.(((..(((((((.((((((((((((((.....)))))))...)))).)))..)).....))))).)))...)))...--- ( -30.50)
>DroEre_CAF1 7828 97 + 1
AGAGAACAGCGCAAGCGAAUCAUA--------------GAGGCGGGAUCAAGGGCAGCA---------UGGUCAUGAUCAGCGAGCAUGCAGCUCAAGAUGCUUAGCCGAGUGGCCGAGG
........((....))...((((.--------------..(((((.(((..((((.(((---------((.((.........)).))))).))))..))).))..)))..))))...... ( -30.10)
>DroYak_CAF1 6987 94 + 1
AGAGGAGAACGUAAACAAAUCAUA--------------GAGGCGGGAUCAAGGGCAGCA---------UGAUCAUGAUCAGCACGCAUGCAGCUCGAGAUGAUCAGCUGAGUGGCCG---
...((.....(....)...((((.--------------..(((..(((((.((((.(((---------((....((.....))..))))).))))....))))).)))..)))))).--- ( -22.90)
>consensus
AGAGAACAGCGUAAACAAAUCACAAA________AA_CGAGGCGGGAUCAAGGGCAGCAUGAUCAUGAUGAUCAUGAUCACCAAGCAUGCAGCUCAAGAUGAUCAGCCGAAUGGCCG___
........................................(((..(((((.((((.(((((.......((((....)))).....))))).))))....))))).)))............ (-18.46 = -19.14 +   0.68)

alignment

secondary structure

dotplot

Window 7

Location	6,592,024 – 6,592,141
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.21
Mean single sequence MFE	-42.26
Consensus MFE	-28.04
Energy contribution	-28.64
Covariance contribution	0.60
Combinations/Pair	1.24
Mean z-score	-2.70
Structure conservation index	0.66
SVM decision value	1.54
SVM RNA-class probability	0.962334
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6592024 117 + 22224390
GGCGGGAUCAAGGGUAGCGUGAUCAUGAUGAUCAUGAUCAUCAAGCAUGCAGCUCAAGAUGAUCAGCCGAAUGGCCG---UGACUAUGGCCAGCCAGAAUGGAUCUAUUCGAGAUGAGAA
(((..(((((.((((.(((((....(((((((....)))))))..))))).))))....))))).)))(..((((((---(....)))))))..).(((((....))))).......... ( -43.20)
>DroSec_CAF1 7696 117 + 1
GGCGGGAUCAAGGGCAGCCUGAUCAUGAUGAUCAUGAUCACCAGGCAUGCAGCUCAAGAUGAUCCGCCGAAUGGCCG---UGACUAUGGCCAACCAGAAUGGAUCUAUUCGAGAUGAGAA
(((((.((((((.((((((((((((((.....)))))))...)))).)))..)).....)))))))))...((((((---(....)))))))....(((((....))))).......... ( -44.10)
>DroSim_CAF1 4504 117 + 1
GGCGGGAUCAAGGGCAGCCUGAUCAUGAUGAUCAUGAUCACCAGGCAUGCAGCUCAAGAUGAUCAGCCGAAUGGCCG---UGACUAUGGCCAGCCAGAAUGGAUCUAUUCGAGAUGAGAA
(((..(((((((.((((((((((((((.....)))))))...)))).)))..)).....))))).)))(..((((((---(....)))))))..).(((((....))))).......... ( -42.60)
>DroEre_CAF1 7854 111 + 1
GGCGGGAUCAAGGGCAGCA---------UGGUCAUGAUCAGCGAGCAUGCAGCUCAAGAUGCUUAGCCGAGUGGCCGAGGUGACUGCGGCUGGCCAGAACUGAGCUAUUCGCGAAAGGAA
(((((.(((..((((.(((---------((.((.........)).))))).))))..))).))..)))(((((((((((....)).)))))(((((....)).))))))).(....)... ( -42.00)
>DroYak_CAF1 7013 108 + 1
GGCGGGAUCAAGGGCAGCA---------UGAUCAUGAUCAGCACGCAUGCAGCUCGAGAUGAUCAGCUGAGUGGCCG---UGACUGUGGCCAGUCAGAAUGGAACUAUUCGAGCAAAGGA
.(((.(((((.(..(....---------.)..).)))))....))).....(((((((..(.((..((((.((((((---......)))))).))))....)).)..)))))))...... ( -39.40)
>consensus
GGCGGGAUCAAGGGCAGCAUGAUCAUGAUGAUCAUGAUCACCAAGCAUGCAGCUCAAGAUGAUCAGCCGAAUGGCCG___UGACUAUGGCCAGCCAGAAUGGAUCUAUUCGAGAUGAGAA
(((..(((((.((((.(((((.......((((....)))).....))))).))))....))))).)))(..((((((.........))))))..).(((((....))))).......... (-28.04 = -28.64 +   0.60)

alignment

secondary structure

dotplot

Window 8

Location	6,592,024 – 6,592,141
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.21
Mean single sequence MFE	-34.54
Consensus MFE	-21.22
Energy contribution	-23.26
Covariance contribution	2.04
Combinations/Pair	1.19
Mean z-score	-1.88
Structure conservation index	0.61
SVM decision value	0.07
SVM RNA-class probability	0.567388
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6592024 117 - 22224390
UUCUCAUCUCGAAUAGAUCCAUUCUGGCUGGCCAUAGUCA---CGGCCAUUCGGCUGAUCAUCUUGAGCUGCAUGCUUGAUGAUCAUGAUCAUCAUGAUCACGCUACCCUUGAUCCCGCC
..........(((((((.....))))..(((((.......---.))))))))(((.(((((..(..(((.....)))..)((((((((.....)))))))).........)))))..))) ( -34.50)
>DroSec_CAF1 7696 117 - 1
UUCUCAUCUCGAAUAGAUCCAUUCUGGUUGGCCAUAGUCA---CGGCCAUUCGGCGGAUCAUCUUGAGCUGCAUGCCUGGUGAUCAUGAUCAUCAUGAUCAGGCUGCCCUUGAUCCCGCC
...(((.(((((...(((((...(((..(((((.......---.)))))..))).)))))...)))))..(((.((((...(((((((.....))))))))))))))...)))....... ( -40.70)
>DroSim_CAF1 4504 117 - 1
UUCUCAUCUCGAAUAGAUCCAUUCUGGCUGGCCAUAGUCA---CGGCCAUUCGGCUGAUCAUCUUGAGCUGCAUGCCUGGUGAUCAUGAUCAUCAUGAUCAGGCUGCCCUUGAUCCCGCC
...(((.(((((...((((....(((..(((((.......---.)))))..)))..))))...)))))..(((.((((...(((((((.....))))))))))))))...)))....... ( -37.10)
>DroEre_CAF1 7854 111 - 1
UUCCUUUCGCGAAUAGCUCAGUUCUGGCCAGCCGCAGUCACCUCGGCCACUCGGCUAAGCAUCUUGAGCUGCAUGCUCGCUGAUCAUGACCA---------UGCUGCCCUUGAUCCCGCC
........(((...(((((((.....((.(((((.(((..(....)..))))))))..))...)))))))(((((.(((.......))).))---------)))............))). ( -30.50)
>DroYak_CAF1 7013 108 - 1
UCCUUUGCUCGAAUAGUUCCAUUCUGACUGGCCACAGUCA---CGGCCACUCAGCUGAUCAUCUCGAGCUGCAUGCGUGCUGAUCAUGAUCA---------UGCUGCCCUUGAUCCCGCC
......((((((.....((....((((.(((((.......---.))))).))))..)).....)))))).(((((((((.....))))..))---------)))................ ( -29.90)
>consensus
UUCUCAUCUCGAAUAGAUCCAUUCUGGCUGGCCAUAGUCA___CGGCCAUUCGGCUGAUCAUCUUGAGCUGCAUGCCUGCUGAUCAUGAUCAUCAUGAUCAGGCUGCCCUUGAUCCCGCC
.......(((((...((((....((((.(((((...........))))).))))..))))...)))))..(((.((((((((((....)))))))......))))))............. (-21.22 = -23.26 +   2.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:44 2006