Locus 4143

Sequence ID	X_DroMel_CAF1
Location	10,870,721 – 10,870,891
Length	170
Max. P	0.869831

overview

Window 5

Location	10,870,721 – 10,870,832
Length	111
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	93.96
Mean single sequence MFE	-41.50
Consensus MFE	-36.76
Energy contribution	-37.56
Covariance contribution	0.80
Combinations/Pair	1.06
Mean z-score	-1.42
Structure conservation index	0.89
SVM decision value	0.87
SVM RNA-class probability	0.869831
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10870721 111 - 22224390
UACGCAGCGUUGUAC-------GUUGUACAUUGCUGGUAAAAACGCGGCCAACGUCAAAGGCAAAUGGCUCAAGUGGUGGGCGUUUGACAAGAGCGGGCGUGGCAGUGGGCGGCGGGG-
(((.(((((.(((((-------...))))).))))))))....(((.(((.((((((((.((..((.((....)).))..)).))))))....((.......)).)).))).)))...- ( -43.10)
>DroSec_CAF1 25295 111 - 1
UACGCAGCGUUGUAC-------GUUGUACAUUGCUGGUAAAAACGCGACCAACGUCAAAGGCAAAUGGCUCAAGUGGUGGGCGUUUGACAAGAGCGGGCGUGGCAGUGGGCGGCGGGG-
(((.(((((.(((((-------...))))).))))))))....(.((.((...((((((.((..((.((....)).))..)).))))))....((..((......))..)))))).).- ( -37.70)
>DroSim_CAF1 26714 111 - 1
UACGCAGCGUUGUAC-------GUUGUACAUUGCUGGUAAAAACGCGGCCAACGUCAAAGGCAAAUGGCUCAAGUGGUGGGCGUUUGACAAGAGCGGGCGUGGCAGCGGGCGGCGGGG-
(((.(((((.(((((-------...))))).))))))))....(((.(((...((((((.((..((.((....)).))..)).))))))....((..((...)).)).))).)))...- ( -43.40)
>DroEre_CAF1 1725 111 - 1
UACGCAGCGUUGUAC-------GUUGUACACUGCUGGCAAAAACGCGGCCAACGUCAAAGGCAAAUGGCUCAAGUGGUGGGCGUUCGACAAGAGCGGGCGUGGCAGGGGGCGGUGGGG-
...((((((.....)-------))))).(((((((.((......)).((((.((((...........(((((.....)))))((((.....)))).))))))))....)))))))...- ( -41.20)
>DroYak_CAF1 25184 119 - 1
UACGCAGCGUUGUACGUUGUACGUUGUACAUUGCUGGUAAAAACGCGGCCAACGUCAAAGGCAAACGGCUCAAGUGGAGGGCGUUUGACAAGAGCGGGCGUGGCAGUGGGCGGUGGGGG
(((.(((((.((((((........)))))).))))))))....(((.(((.((((((((.((...(.((....)).)...)).))))))....((.......)).)).))).))).... ( -42.10)
>consensus
UACGCAGCGUUGUAC_______GUUGUACAUUGCUGGUAAAAACGCGGCCAACGUCAAAGGCAAAUGGCUCAAGUGGUGGGCGUUUGACAAGAGCGGGCGUGGCAGUGGGCGGCGGGG_
(((.(((((.(((((..........))))).))))))))....(((.(((.((((((((.((..((.((....)).))..)).))))))....((.......)).)).))).))).... (-36.76 = -37.56 +   0.80)

alignment

secondary structure

dotplot

Window 6

Location	10,870,760 – 10,870,870
Length	110
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.35
Mean single sequence MFE	-31.22
Consensus MFE	-21.15
Energy contribution	-22.46
Covariance contribution	1.31
Combinations/Pair	1.25
Mean z-score	-1.87
Structure conservation index	0.68
SVM decision value	0.26
SVM RNA-class probability	0.657014
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10870760 110 + 22224390
CACCACUUGAGCCAUUUGCCUUUGACGUUGGCCGCGUUUUUAC-CAGCAAUGUACAAC-------GUACAACGCUGCGUAUGCGCAUUAU--UUGAAACGAGCACAGUGGAAACAUUUCU
..(((((.(.(((....(((.........))).((((...(((-((((..(((((...-------)))))..)))).))).)))).....--.......).)).)))))).......... ( -30.50)
>DroSec_CAF1 25334 110 + 1
CACCACUUGAGCCAUUUGCCUUUGACGUUGGUCGCGUUUUUAC-CAGCAAUGUACAAC-------GUACAACGCUGCGUAUGCGCAUUAU--UUGAAACGAGCACAGUGGAAACAUUUCU
..(((((.(.(((..........(((....)))((((...(((-((((..(((((...-------)))))..)))).))).)))).....--.......).)).)))))).......... ( -29.70)
>DroSim_CAF1 26753 110 + 1
CACCACUUGAGCCAUUUGCCUUUGACGUUGGCCGCGUUUUUAC-CAGCAAUGUACAAC-------GUACAACGCUGCGUAUGCGCAUUAU--UUGAAACGAGCACAGUGGAAACAUUUCU
..(((((.(.(((....(((.........))).((((...(((-((((..(((((...-------)))))..)))).))).)))).....--.......).)).)))))).......... ( -30.50)
>DroEre_CAF1 1764 110 + 1
CACCACUUGAGCCAUUUGCCUUUGACGUUGGCCGCGUUUUUGC-CAGCAGUGUACAAC-------GUACAACGCUGCGUAUGCGCAUUAU--UUGAAACGAGCACAGUGGAAACAUUUUU
..(((((.(.(((....(((.........))).((((...(((-((((..(((((...-------)))))..)))).))).)))).....--.......).)).)))))).......... ( -31.80)
>DroYak_CAF1 25224 117 + 1
CUCCACUUGAGCCGUUUGCCUUUGACGUUGGCCGCGUUUUUAC-CAGCAAUGUACAACGUACAACGUACAACGCUGCGUAUGCGCAUUAU--UUGAAACGAGCACAGUGGAAACAUUUCU
.((((((.(.((((((((((.........))).((((...(((-((((..(((((..........)))))..)))).))).)))).....--...))))).)).)))))))......... ( -37.40)
>DroPer_CAF1 47133 88 + 1
CAGC--------------------ACGGUGGCCGUGCUUUCGCCCAACAAUGU----C-------GU-CAUUGUUACGAAUGCGCAUUACACAUCGAAGCAGCACAGUGGAAACACUUUU
..((--------------------.(((((...((((.((((...(((((((.----.-------..-))))))).)))).))))......)))))..)).....((((....))))... ( -27.40)
>consensus
CACCACUUGAGCCAUUUGCCUUUGACGUUGGCCGCGUUUUUAC_CAGCAAUGUACAAC_______GUACAACGCUGCGUAUGCGCAUUAU__UUGAAACGAGCACAGUGGAAACAUUUCU
.....((((.((((..............)))).((((...(((.((((..(((((..........)))))..)))).))).)))).............))))...((((....))))... (-21.15 = -22.46 +   1.31)

alignment

secondary structure

dotplot

Window 7

Location	10,870,800 – 10,870,891
Length	91
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	75.37
Mean single sequence MFE	-26.50
Consensus MFE	-16.40
Energy contribution	-17.59
Covariance contribution	1.20
Combinations/Pair	1.16
Mean z-score	-1.60
Structure conservation index	0.62
SVM decision value	0.77
SVM RNA-class probability	0.846189
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10870800 91 + 22224390
UAC-CAGCAAUGUACAAC-------GUACAACGCUGCGUAUGCGCAUUAU--UUGAAACGAGCACAGUGGAAACAUUUCUGC-------ACAGCAACUGUGUGUGUGU
(((-((((..(((((...-------)))))..)))).))).((((((...--.........(((.((((....))))..)))-------((((...)))))))))).. ( -25.00)
>DroPse_CAF1 46896 93 + 1
CGCCCAACAAUGU----C-------GU-CAUUGUUACGAAUGCGCAUUACACAUCGAAGCAGCACAGUGGAAACACUUUUGCCAACGGUAAAACGGCUGUGUGCG---
(((.((((((((.----.-------..-))))))).(((.((.(.....).)))))..(((((..((((....))))((((((...))))))...)))))).)))--- ( -26.60)
>DroSim_CAF1 26793 91 + 1
UAC-CAGCAAUGUACAAC-------GUACAACGCUGCGUAUGCGCAUUAU--UUGAAACGAGCACAGUGGAAACAUUUCUGC-------ACAGCAACUGUGUGUGUGU
(((-((((..(((((...-------)))))..)))).))).((((((...--.........(((.((((....))))..)))-------((((...)))))))))).. ( -25.00)
>DroEre_CAF1 1804 91 + 1
UGC-CAGCAGUGUACAAC-------GUACAACGCUGCGUAUGCGCAUUAU--UUGAAACGAGCACAGUGGAAACAUUUUUGC-------ACAGCCACUGUGUAUGUGC
(((-((((..(((((...-------)))))..)))).))).((((((...--.........(((((((((...((....)).-------....))))))))))))))) ( -30.10)
>DroYak_CAF1 25264 98 + 1
UAC-CAGCAAUGUACAACGUACAACGUACAACGCUGCGUAUGCGCAUUAU--UUGAAACGAGCACAGUGGAAACAUUUCUGC-------ACAGCGACUGUGUGUGUGU
(((-((((..(((((..........)))))..)))).))).((((((...--.........(((.((((....))))..)))-------((((...)))))))))).. ( -25.70)
>DroPer_CAF1 47153 93 + 1
CGCCCAACAAUGU----C-------GU-CAUUGUUACGAAUGCGCAUUACACAUCGAAGCAGCACAGUGGAAACACUUUUGCCAACGGUAAAACGGCUGUGUGCG---
(((.((((((((.----.-------..-))))))).(((.((.(.....).)))))..(((((..((((....))))((((((...))))))...)))))).)))--- ( -26.60)
>consensus
UAC_CAGCAAUGUACAAC_______GUACAACGCUGCGUAUGCGCAUUAU__UUGAAACGAGCACAGUGGAAACAUUUCUGC_______ACAGCGACUGUGUGUGUGU
(((.((((..(((((..........)))))..)))).))).((((((..............(((.((((....))))..)))................)))))).... (-16.40 = -17.59 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:25 2006