Locus 5325

Sequence ID	2L_DroMel_CAF1
Location	15,063,411 – 15,063,541
Length	130
Max. P	0.952140

overview

Window 7

Location	15,063,411 – 15,063,501
Length	90
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	78.06
Mean single sequence MFE	-43.05
Consensus MFE	-20.78
Energy contribution	-20.73
Covariance contribution	-0.05
Combinations/Pair	1.35
Mean z-score	-2.70
Structure conservation index	0.48
SVM decision value	1.42
SVM RNA-class probability	0.952140
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15063411 90 + 22407834
---CUGCAG------CAG------CAGCUG---ACGGUUGCUUCUUCUUGCCAGCUGCUG---CUGCG------GCAGCAGCGGCCGUCGGCGCCACAAGAUUAUCUAAUGGAUCGC
---.(((..------..)------))((((---((((((((........))..(((((((---(....------)))))))))))))))))).(((..((.....))..)))..... ( -39.90)
>DroSec_CAF1 7750 90 + 1
---CUGCAG------CAG------CAGCUG---ACGGCUGCUUCUUCUUGCCAGCUGCUG---CUACG------GCAGCAGCGGCCGUCGGCGCCACAAGAUUAUCUAAUGGAUCGC
---.(((..------..)------))((((---((((((((........))..(((((((---(....------)))))))))))))))))).(((..((.....))..)))..... ( -44.90)
>DroEre_CAF1 8249 90 + 1
---CUGCAG---------------CAGCUG---ACGUCUGCUUCUUCUUGCCAGCUGCUGCUGCUGCA------GCAGCGGCGGCCGUCGGCGCCACAAGAUUAUCUAAUGGAUCGC
---.....(---------------(.((((---(((...((........))..(((((((((((....------)))))))))))))))))).(((..((.....))..)))...)) ( -38.40)
>DroYak_CAF1 7915 87 + 1
---CUGCAG---------------CAGCUG---ACGGCUGCUUCUUCUUGCCAGCUGCUG---CUGCG------GCAGCGGCGGCCGUCGGCGCCACAAGAUUAUCUAAUGGAUCGC
---.....(---------------(.((((---((((((((........))..(((((((---(....------)))))))))))))))))).(((..((.....))..)))...)) ( -40.90)
>DroAna_CAF1 8696 102 + 1
---AUGCAG------CACCACCCGUAGCAG---UCGUCUGCUUCUUCUUGCCAGCUGCGG---CUGCUGCCGUUGCUGCUGCGGCCGUCGGCGCCACAAGAUUAUCUAAUGGAUCGC
---..((((------((.((.(.(((((((---((((..(((..........))).))))---))))))).).)).))))))((((....).)))....((((........)))).. ( -39.30)
>DroPer_CAF1 7500 111 + 1
CCGAUGCGGCGGCAGCACCGCCCGCGGCAGGCUGUGGCUGCUUCUUCUUGCUGGCUGCUG---UUGCG---GCUGCUACGGCAGCGGUCGCCGCCACAAGAUUAUCUAAUGGUUCGG
((((.(((((.(((((.(((....)))...))))).)))))....(((((.((((.((..---..((.---(((((....))))).)).)).)))))))))............)))) ( -54.90)
>consensus
___CUGCAG______CA_______CAGCUG___ACGGCUGCUUCUUCUUGCCAGCUGCUG___CUGCG______GCAGCGGCGGCCGUCGGCGCCACAAGAUUAUCUAAUGGAUCGC
.....((.................((((((....)))))).........(((.(((((((...((((.......)))))))))))....))))).....((((........)))).. (-20.78 = -20.73 +  -0.05)

alignment

secondary structure

dotplot

Window 8

Location	15,063,411 – 15,063,501
Length	90
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	78.06
Mean single sequence MFE	-41.08
Consensus MFE	-18.92
Energy contribution	-18.90
Covariance contribution	-0.02
Combinations/Pair	1.14
Mean z-score	-2.30
Structure conservation index	0.46
SVM decision value	0.55
SVM RNA-class probability	0.778561
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15063411 90 - 22407834
GCGAUCCAUUAGAUAAUCUUGUGGCGCCGACGGCCGCUGCUGC------CGCAG---CAGCAGCUGGCAAGAAGAAGCAACCGU---CAGCUG------CUG------CUGCAG---
(((..((((.((.....)).))))))).(.((((....)))).------)((((---(((((((((((..............))---))))))------)))------))))..--- ( -42.24)
>DroSec_CAF1 7750 90 - 1
GCGAUCCAUUAGAUAAUCUUGUGGCGCCGACGGCCGCUGCUGC------CGUAG---CAGCAGCUGGCAAGAAGAAGCAGCCGU---CAGCUG------CUG------CUGCAG---
(((..((((.((.....)).))))))).((((((.((((((((------....)---)))))))..((........)).)))))---)..(((------(..------..))))--- ( -40.30)
>DroEre_CAF1 8249 90 - 1
GCGAUCCAUUAGAUAAUCUUGUGGCGCCGACGGCCGCCGCUGC------UGCAGCAGCAGCAGCUGGCAAGAAGAAGCAGACGU---CAGCUG---------------CUGCAG---
((..............((((((((((((...)).))))(((((------(((....))))))))..))))))...(((((.(..---..))))---------------))))..--- ( -39.20)
>DroYak_CAF1 7915 87 - 1
GCGAUCCAUUAGAUAAUCUUGUGGCGCCGACGGCCGCCGCUGC------CGCAG---CAGCAGCUGGCAAGAAGAAGCAGCCGU---CAGCUG---------------CUGCAG---
((((((.....)))......((((((((...)).))))))...------))).(---(((((((((((..............))---))))))---------------))))..--- ( -38.54)
>DroAna_CAF1 8696 102 - 1
GCGAUCCAUUAGAUAAUCUUGUGGCGCCGACGGCCGCAGCAGCAACGGCAGCAG---CCGCAGCUGGCAAGAAGAAGCAGACGA---CUGCUACGGGUGGUG------CUGCAU---
(((..((((..(....((((((.(((((...)).)))..((((..((((....)---)))..))))))))))...(((((....---))))).)..))))..------.)))..--- ( -38.00)
>DroPer_CAF1 7500 111 - 1
CCGAACCAUUAGAUAAUCUUGUGGCGGCGACCGCUGCCGUAGCAGC---CGCAA---CAGCAGCCAGCAAGAAGAAGCAGCCACAGCCUGCCGCGGGCGGUGCUGCCGCCGCAUCGG
((((..(((.((.....)).)))((((((...(((((.((.((...---.)).)---).)))))............(((((.((.(((((...))))).))))))))))))).)))) ( -48.20)
>consensus
GCGAUCCAUUAGAUAAUCUUGUGGCGCCGACGGCCGCCGCUGC______CGCAG___CAGCAGCUGGCAAGAAGAAGCAGCCGU___CAGCUG_______UG______CUGCAG___
(((..((((.((.....)).))))))).....(((((.((((...............)))).)).)))........((((............................))))..... (-18.92 = -18.90 +  -0.02)

alignment

secondary structure

dotplot

Window 9

Location	15,063,433 – 15,063,541
Length	108
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	81.32
Mean single sequence MFE	-38.58
Consensus MFE	-20.97
Energy contribution	-22.05
Covariance contribution	1.08
Combinations/Pair	1.23
Mean z-score	-3.20
Structure conservation index	0.54
SVM decision value	1.12
SVM RNA-class probability	0.918330
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15063433 108 + 22407834
CUUCUUCUUGCCAGCUGCUG---CUGCG------GCAGCAGCGGCCGUCGGCGCCACAAGAUUAUCUAAUGGAUCGCUGACAUCGUCGUCCAUGAACAAAAGUUCAUAACGAUUUUU
.........(((.(((((((---(....------))))))))))).((((((((((..((.....))..)))..)))))))...(((((..((((((....)))))).))))).... ( -45.20)
>DroPse_CAF1 7247 111 + 1
CUUCUUCUUGCUGGCUGCUG---UUGCG---GCUGCUACGGCAGCGGUCGCCGCCACAAGAUUAUCUAAUGGUUCGGAAACAUCAUCGUCCAUGAACAAGAGUUCAUAACGAUUUUU
.....(((((.((((.((..---..((.---(((((....))))).)).)).)))))))))..............(....)...(((((..((((((....)))))).))))).... ( -38.80)
>DroEre_CAF1 8268 111 + 1
CUUCUUCUUGCCAGCUGCUGCUGCUGCA------GCAGCGGCGGCCGUCGGCGCCACAAGAUUAUCUAAUGGAUCGCUGACAUCGUCGUCCAUGAACAAAAGUUCAUAACGAUUUUU
.........(((.((((((((((...))------))))))))))).((((((((((..((.....))..)))..)))))))...(((((..((((((....)))))).))))).... ( -46.80)
>DroMoj_CAF1 7023 91 + 1
-------UUGAUGGCUGCUG---CUUCU----------------UCUUGGCCGCGACAAGAUUAUCUAAUGGAUCGCCAACAUCGUCGUCCAUGAACAAGAGUUCAUAACGAUUUUU
-------.((.(((((((.(---((...----------------....))).)))....((((........)))))))).))..(((((..((((((....)))))).))))).... ( -23.60)
>DroAna_CAF1 8724 114 + 1
CUUCUUCUUGCCAGCUGCGG---CUGCUGCCGUUGCUGCUGCGGCCGUCGGCGCCACAAGAUUAUCUAAUGGAUCGCUGACAUCGUCGUCCAUGAACAAGAGCUCAUAACGAUUUUU
....((((((.((((.((((---(....))))).))))..(((((.((((((((((..((.....))..)))..)))))))...))))).......))))))............... ( -38.30)
>DroPer_CAF1 7540 111 + 1
CUUCUUCUUGCUGGCUGCUG---UUGCG---GCUGCUACGGCAGCGGUCGCCGCCACAAGAUUAUCUAAUGGUUCGGAAACAUCAUCGUCCAUGAACAAGAGUUCAUAACGAUUUUU
.....(((((.((((.((..---..((.---(((((....))))).)).)).)))))))))..............(....)...(((((..((((((....)))))).))))).... ( -38.80)
>consensus
CUUCUUCUUGCCAGCUGCUG___CUGCG______GCUGCGGCGGCCGUCGCCGCCACAAGAUUAUCUAAUGGAUCGCUAACAUCGUCGUCCAUGAACAAGAGUUCAUAACGAUUUUU
.............(((((((.....((.......))..))))))).((.(((((((..((.....))..)))..)))).))...(((((..((((((....)))))).))))).... (-20.97 = -22.05 +   1.08)

alignment

secondary structure

dotplot

Window 0

Location	15,063,433 – 15,063,541
Length	108
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	81.32
Mean single sequence MFE	-36.65
Consensus MFE	-22.70
Energy contribution	-23.57
Covariance contribution	0.86
Combinations/Pair	1.16
Mean z-score	-2.39
Structure conservation index	0.62
SVM decision value	0.70
SVM RNA-class probability	0.827820
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15063433 108 - 22407834
AAAAAUCGUUAUGAACUUUUGUUCAUGGACGACGAUGUCAGCGAUCCAUUAGAUAAUCUUGUGGCGCCGACGGCCGCUGCUGC------CGCAG---CAGCAGCUGGCAAGAAGAAG
.....(((((((((((....)))))).)))))...((((.(((..((((.((.....)).))))))).))))(((((((((((------....)---))))))).)))......... ( -44.80)
>DroPse_CAF1 7247 111 - 1
AAAAAUCGUUAUGAACUCUUGUUCAUGGACGAUGAUGUUUCCGAACCAUUAGAUAAUCUUGUGGCGGCGACCGCUGCCGUAGCAGC---CGCAA---CAGCAGCCAGCAAGAAGAAG
....((((((((((((....)))))).))))))...(((.(((..((((.((.....)).))))))).))).(((((.((.((...---.)).)---).)))))............. ( -34.10)
>DroEre_CAF1 8268 111 - 1
AAAAAUCGUUAUGAACUUUUGUUCAUGGACGACGAUGUCAGCGAUCCAUUAGAUAAUCUUGUGGCGCCGACGGCCGCCGCUGC------UGCAGCAGCAGCAGCUGGCAAGAAGAAG
.....(((((((((((....)))))).)))))...((((.(((..((((.((.....)).))))))).))))...((((((((------(((....)))))))).)))......... ( -45.60)
>DroMoj_CAF1 7023 91 - 1
AAAAAUCGUUAUGAACUCUUGUUCAUGGACGACGAUGUUGGCGAUCCAUUAGAUAAUCUUGUCGCGGCCAAGA----------------AGAAG---CAGCAGCCAUCAA-------
.....(((((((((((....)))))).)))))...((.((((.........((((....))))((.((.....----------------....)---).)).)))).)).------- ( -23.10)
>DroAna_CAF1 8724 114 - 1
AAAAAUCGUUAUGAGCUCUUGUUCAUGGACGACGAUGUCAGCGAUCCAUUAGAUAAUCUUGUGGCGCCGACGGCCGCAGCAGCAACGGCAGCAG---CCGCAGCUGGCAAGAAGAAG
.....(((((((((((....)))))).)))))...(((((((...((((.((.....)).))))....(.((((.((.((.......)).)).)---)))).)))))))........ ( -38.20)
>DroPer_CAF1 7540 111 - 1
AAAAAUCGUUAUGAACUCUUGUUCAUGGACGAUGAUGUUUCCGAACCAUUAGAUAAUCUUGUGGCGGCGACCGCUGCCGUAGCAGC---CGCAA---CAGCAGCCAGCAAGAAGAAG
....((((((((((((....)))))).))))))...(((.(((..((((.((.....)).))))))).))).(((((.((.((...---.)).)---).)))))............. ( -34.10)
>consensus
AAAAAUCGUUAUGAACUCUUGUUCAUGGACGACGAUGUCAGCGAUCCAUUAGAUAAUCUUGUGGCGCCGACGGCCGCCGCAGC______CGCAG___CAGCAGCCAGCAAGAAGAAG
.....(((((((((((....)))))).)))))...(((((((..................(((((.......))))).............((.......)).)))))))........ (-22.70 = -23.57 +   0.86)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:25 2006