Locus 7573

Sequence ID	2L_DroMel_CAF1
Location	20,948,767 – 20,948,868
Length	101
Max. P	0.995779

overview

Window 9

Location	20,948,767 – 20,948,868
Length	101
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	70.64
Mean single sequence MFE	-35.22
Consensus MFE	-20.30
Energy contribution	-20.97
Covariance contribution	0.67
Combinations/Pair	1.17
Mean z-score	-2.52
Structure conservation index	0.58
SVM decision value	2.61
SVM RNA-class probability	0.995779
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20948767 101 + 22407834
UUGGAGU-------GC-GCCGAAGAUGUUGAUAUUAUGCCACCGGUGUGGCGCAUAAUGCAGCUUAUCUGGGGAAUUAGGCAAGGAAUCUGGGAAGGCUGACGAAAGCG----------
.....((-------((-(((...((((....))))(((((...))))))))))))....((((((.((..((...((.....))...))..)).)))))).(....)..---------- ( -25.70)
>DroVir_CAF1 21575 105 + 1
UUGGCGUUAGGCCUGCGUCUGGGCUGGUUGUUAUUAUGCGCCCAGCGUGGCGCAUAAUGCAGCUAAUCUGGGGAAUUAGGUAAA---------AAAGCUGACAAAAGGCAA-----ACA
(..((.....(((((..((..(..(((((((.((((((((((......)))))))))))))))))..)..))....)))))...---------...))..)..........-----... ( -38.70)
>DroPse_CAF1 43641 96 + 1
---UCCC-------GCUGCAAGCCGGGCUGUUAUUAUGCGCCCGGUGUGGCGCAUAAUGCAGCUAAUCUAGGGAAUUAGGUAAAA--------AGGGCUGACAAAAGCCAA-----ACA
---((((-------((.....))..((((((.((((((((((......))))))))))))))))......))))...........--------..((((......))))..-----... ( -38.10)
>DroYak_CAF1 13134 101 + 1
UUGGAGU-------GC-GCUGUAGAUGUGGAUAUUAUGCCACCGGUGUGGCGCAUAAUGCAGCUUAUCUGGGGAAUUAGACAAGGAAUCAGGGAAGGCUGACGAAAGCA----------
.....((-------((-((..((...((((........))))...))..))))))....((((((.(((((....((....))....)))))..)))))).(....)..---------- ( -28.80)
>DroAna_CAF1 37066 102 + 1
ACGGAGA-------UG-CCAGGCCAUGUUGUUAUUAUGCGUCCGGUGUGGCGCAUAAUGCAGCUAAUCUGGGGAAUUAGGUAA---------AAAGGCUGACAAAAGCCCGGCAAGGCA
.......-------((-((..(((..(((((.((((((((((......)))))))))))))))..((((((....))))))..---------...((((......)))).)))..)))) ( -37.90)
>DroPer_CAF1 34602 99 + 1
CCGGCCC-------GCUGCCAGCCGGGCUGUUAUUAUGCGCCCGGUGUGGCGCAUAAUGCAGCUAAUCUAGGGAAUUAGGUAAAA--------AGGGCUGACAAAAGCCAA-----ACA
..(((..-------..((.(((((.((((((.((((((((((......)))))))))))))))).((((((....))))))....--------..))))).))...)))..-----... ( -42.10)
>consensus
UUGGAGU_______GC_GCAGGCCAGGUUGUUAUUAUGCGCCCGGUGUGGCGCAUAAUGCAGCUAAUCUGGGGAAUUAGGUAAA_________AAGGCUGACAAAAGCCAA_____ACA
..........................((((.(((((((((((......)))))))))))))))..((((((....))))))...............(((......)))........... (-20.30 = -20.97 +   0.67)

alignment

secondary structure

dotplot

Window 0

Location	20,948,767 – 20,948,868
Length	101
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	70.64
Mean single sequence MFE	-29.61
Consensus MFE	-11.71
Energy contribution	-12.04
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.67
Structure conservation index	0.40
SVM decision value	2.44
SVM RNA-class probability	0.994027
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20948767 101 - 22407834
----------CGCUUUCGUCAGCCUUCCCAGAUUCCUUGCCUAAUUCCCCAGAUAAGCUGCAUUAUGCGCCACACCGGUGGCAUAAUAUCAACAUCUUCGGC-GC-------ACUCCAA
----------...........(((..............((.((((....(((.....))).)))).))(((((....))))).................)))-..-------....... ( -17.50)
>DroVir_CAF1 21575 105 - 1
UGU-----UUGCCUUUUGUCAGCUUU---------UUUACCUAAUUCCCCAGAUUAGCUGCAUUAUGCGCCACGCUGGGCGCAUAAUAACAACCAGCCCAGACGCAGGCCUAACGCCAA
.((-----(.((((..((((.(((..---------.....((((((.....))))))....((((((((((......)))))))))).......)))...)))).))))..)))..... ( -29.40)
>DroPse_CAF1 43641 96 - 1
UGU-----UUGGCUUUUGUCAGCCCU--------UUUUACCUAAUUCCCUAGAUUAGCUGCAUUAUGCGCCACACCGGGCGCAUAAUAACAGCCCGGCUUGCAGC-------GGGA---
...-----(((((....)))))(((.--------......(((......)))....(((((((((((((((......))))))))))...(((...))).)))))-------))).--- ( -33.20)
>DroYak_CAF1 13134 101 - 1
----------UGCUUUCGUCAGCCUUCCCUGAUUCCUUGUCUAAUUCCCCAGAUAAGCUGCAUUAUGCGCCACACCGGUGGCAUAAUAUCCACAUCUACAGC-GC-------ACUCCAA
----------(((....(((((......)))))..(((((((........)))))))..)))...(((((.......((((........)))).......))-))-------)...... ( -23.04)
>DroAna_CAF1 37066 102 - 1
UGCCUUGCCGGGCUUUUGUCAGCCUUU---------UUACCUAAUUCCCCAGAUUAGCUGCAUUAUGCGCCACACCGGACGCAUAAUAACAACAUGGCCUGG-CA-------UCUCCGU
.....(((((((((.((((........---------....((((((.....))))))....((((((((((.....)).)))))))).))))...)))))))-))-------....... ( -32.10)
>DroPer_CAF1 34602 99 - 1
UGU-----UUGGCUUUUGUCAGCCCU--------UUUUACCUAAUUCCCUAGAUUAGCUGCAUUAUGCGCCACACCGGGCGCAUAAUAACAGCCCGGCUGGCAGC-------GGGCCGG
...-----.(((((((((((((((..--------......(((......)))....((((.((((((((((......))))))))))..))))..))))))))).-------)))))). ( -42.40)
>consensus
UGU_____UUGGCUUUUGUCAGCCUU_________UUUACCUAAUUCCCCAGAUUAGCUGCAUUAUGCGCCACACCGGGCGCAUAAUAACAACAUGGCCAGC_GC_______ACGCCAA
.................(.((((.................................)))))((((((((((.....)).))))))))................................ (-11.71 = -12.04 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:15 2006