Locus 2400

Sequence ID	2L_DroMel_CAF1
Location	6,540,931 – 6,541,074
Length	143
Max. P	0.935705

overview

Window 2

Location	6,540,931 – 6,541,046
Length	115
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.14
Mean single sequence MFE	-24.09
Consensus MFE	-17.31
Energy contribution	-17.70
Covariance contribution	0.39
Combinations/Pair	1.11
Mean z-score	-1.88
Structure conservation index	0.72
SVM decision value	1.08
SVM RNA-class probability	0.911323
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6540931 115 + 22407834
ACACACAC-GCUUACGCACAAUUAUUAACACUUAUUAAUGUUGAGGUUUCCAUAUAUAUGGCACCCCAGGGCUUAAAUUAAAGUCAUCCCGAGUGCCAAACAGCUGCCUCAAGUGC----
........-......((((...((((((......))))))(((((((...........(((((((....(((((......))))).....).)))))).......)))))))))))---- ( -26.37)
>DroVir_CAF1 97613 106 + 1
----------CACACACACAAUUAUUAACACUUAUUAAUGUUGAGGUUUUUAUAUAGAUGGCACCCCAGGGCCUCAAUUAAAGUC--CAAAAGUGCCA-ACAGCUGCCUCAAGUGGCU-U
----------......(((...((((((......))))))(((((((...........((((((....((((..........)))--)....))))))-......))))))))))...-. ( -23.73)
>DroPse_CAF1 13643 103 + 1
-------------AUACACAAUUAUUAACACUUAUUAAUGUUGAGGUUUUUGCGUAUAUGGCACCCCAGGGCUUAAAUUAAAGUCAUCCCAAGUGCCAAACAGCUGCCUCAAGUGC----
-------------...(((...((((((......))))))(((((((....((.....((((((.....(((((......))))).......))))))....)).)))))))))).---- ( -27.40)
>DroGri_CAF1 18036 101 + 1
----------C---UACACAAUUAUUAACACUUAUUAAUGUUGAGGUUUUUA--UAGAUGGCACCCAGGGGCUUCAAUUAAAGCC--CA-AAGUGCCA-ACAGCUGCCUCAAGCGCCAGU
----------.---..........((((((........))))))(((.....--..(.((((((....((((((......)))))--).-..))))))-.).(((......))))))... ( -29.10)
>DroMoj_CAF1 123408 107 + 1
UCA-ACACUCCACACACACAAUUAUUAACACUUAUUAUUGUUGAGGUUUUUAUAUAGAUGGCACCCCUGGGCCUCAAUUAAAUUC--CA--AGUGCCA-ACAGCUGCUUCAA-------U
...-...................................((((((((...........((((((...((((............))--))--.))))))-......)))))))-------) ( -15.53)
>DroAna_CAF1 13945 110 + 1
A-----GC-AUAUACACACAAUUAUUAACACUUAUUAAUGUUGAGGUUUUCGUAUAUAUGGCACCCCAGGGCUUAAAUUAAAGUCAUCCCGAGUGCCAAACAGCUGGCUCAAGUGC----
.-----.(-(((((.((.......((((((........)))))).......)).))))))((((.....(((((......))))).......(.((((......)))).)..))))---- ( -22.44)
>consensus
__________CA_ACACACAAUUAUUAACACUUAUUAAUGUUGAGGUUUUUAUAUAGAUGGCACCCCAGGGCUUAAAUUAAAGUC__CACAAGUGCCA_ACAGCUGCCUCAAGUGC____
........................................(((((((...........((((((.....(((((......))))).......)))))).......)))))))........ (-17.31 = -17.70 +   0.39)

alignment

secondary structure

dotplot

Window 3

Location	6,540,931 – 6,541,046
Length	115
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.14
Mean single sequence MFE	-29.49
Consensus MFE	-18.03
Energy contribution	-18.90
Covariance contribution	0.87
Combinations/Pair	1.27
Mean z-score	-1.75
Structure conservation index	0.61
SVM decision value	0.46
SVM RNA-class probability	0.745637
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6540931 115 - 22407834
----GCACUUGAGGCAGCUGUUUGGCACUCGGGAUGACUUUAAUUUAAGCCCUGGGGUGCCAUAUAUAUGGAAACCUCAACAUUAAUAAGUGUUAAUAAUUGUGCGUAAGC-GUGUGUGU
----((((..((((...((((.((((((((.((..(.(((......)))).)).)))))))).....))))...))))((((((....)))))).........((....))-)))).... ( -33.20)
>DroVir_CAF1 97613 106 - 1
A-AGCCACUUGAGGCAGCUGU-UGGCACUUUUG--GACUUUAAUUGAGGCCCUGGGGUGCCAUCUAUAUAAAAACCUCAACAUUAAUAAGUGUUAAUAAUUGUGUGUGUG----------
.-.(((((..((((....(((-((((((((..(--(.((((....)))).))..)))))))).....)))....))))((((((....)))))).......))).))...---------- ( -27.20)
>DroPse_CAF1 13643 103 - 1
----GCACUUGAGGCAGCUGUUUGGCACUUGGGAUGACUUUAAUUUAAGCCCUGGGGUGCCAUAUACGCAAAAACCUCAACAUUAAUAAGUGUUAAUAAUUGUGUAU-------------
----((((..((((..(((((.((((((((.((..(.(((......)))).)).)))))))).))).)).....))))((((((....)))))).......))))..------------- ( -28.60)
>DroGri_CAF1 18036 101 - 1
ACUGGCGCUUGAGGCAGCUGU-UGGCACUU-UG--GGCUUUAAUUGAAGCCCCUGGGUGCCAUCUA--UAAAAACCUCAACAUUAAUAAGUGUUAAUAAUUGUGUA---G----------
....((((..((((.......-((((((((-.(--((((((....)))))))..))))))))....--......))))((((((....)))))).......)))).---.---------- ( -33.93)
>DroMoj_CAF1 123408 107 - 1
A-------UUGAAGCAGCUGU-UGGCACU--UG--GAAUUUAAUUGAGGCCCAGGGGUGCCAUCUAUAUAAAAACCUCAACAAUAAUAAGUGUUAAUAAUUGUGUGUGUGGAGUGU-UGA
.-------......((((...-(((((((--((--(..(((....)))..)))..)))))))((((((((.........(((((.((........)).))))).))))))))..))-)). ( -23.20)
>DroAna_CAF1 13945 110 - 1
----GCACUUGAGCCAGCUGUUUGGCACUCGGGAUGACUUUAAUUUAAGCCCUGGGGUGCCAUAUAUACGAAAACCUCAACAUUAAUAAGUGUUAAUAAUUGUGUGUAUAU-GC-----U
----((((....(((((....))))).((((((..(.(((......))))))))))))))((((((((((........((((((....))))))........)))))))))-).-----. ( -30.79)
>consensus
____GCACUUGAGGCAGCUGU_UGGCACUUGGG__GACUUUAAUUGAAGCCCUGGGGUGCCAUAUAUAUAAAAACCUCAACAUUAAUAAGUGUUAAUAAUUGUGUGU_UG__________
....((((..((((....(((.((((((((.((....(((......)))..)).)))))))).....)))....))))((((((....)))))).......))))............... (-18.03 = -18.90 +   0.87)

alignment

secondary structure

dotplot

Window 4

Location	6,540,970 – 6,541,074
Length	104
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	78.86
Mean single sequence MFE	-31.65
Consensus MFE	-19.70
Energy contribution	-20.57
Covariance contribution	0.86
Combinations/Pair	1.05
Mean z-score	-2.08
Structure conservation index	0.62
SVM decision value	1.03
SVM RNA-class probability	0.902963
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6540970 104 + 22407834
UUGAGGUUUCCAUAUAUAUGGCACCCCAGGGCUUAAAUUAAAGUCAUCCCGAGUGCCAAACAGCUGCCUCAAGUGC-CGCACUUGAGCCGAUCUGGAUCCCGGAA--------
....((..((((......(((((((....(((((......))))).....).))))))......((.((((((((.-..)))))))).))...))))..))....-------- ( -31.90)
>DroPse_CAF1 13670 100 + 1
UUGAGGUUUUUGCGUAUAUGGCACCCCAGGGCUUAAAUUAAAGUCAUCCCAAGUGCCAAACAGCUGCCUCAAGUGC-CGCACUUGAG----UCUCGCUCCUCGAC--------
((((((.....(((....((((((.....(((((......))))).......)))))).........((((((((.-..))))))))----...))).)))))).-------- ( -32.10)
>DroYak_CAF1 13585 111 + 1
UUGAGGUUUCGAUAUAGAUGGCACCCCAGGGCUUAAAUUAAAGUCAUCCCGAGUGCCAAACAGCUGCCUCAAGUGU-CGCACUUGAGCCGAUCUGGGUCC-GGAAUCCGGAAU
(((.(((((((((.(((((((((((....(((((......))))).....).))))).......((.((((((((.-..)))))))).))))))).)).)-)))))))))... ( -33.70)
>DroMoj_CAF1 123447 91 + 1
UUGAGGUUUUUAUAUAGAUGGCACCCCUGGGCCUCAAUUAAAUUC--CA--AGUGCCA-ACAGCUGCUUCAA----UCGCACUUCAGCCCCUGUUGGCCC-------------
....((..((((....((.(((.((...)))))))...))))..)--).--...((((-((((..(((....----.........)))..))))))))..------------- ( -24.62)
>DroAna_CAF1 13979 98 + 1
UUGAGGUUUUCGUAUAUAUGGCACCCCAGGGCUUAAAUUAAAGUCAUCCCGAGUGCCAAACAGCUGGCUCAAGUGC-GGCACUUGAGCCGAUCAUCAUC--------------
....(((..((.......(((((((....(((((......))))).....).)))))).......((((((((((.-..))))))))))))..)))...-------------- ( -33.00)
>DroPer_CAF1 13701 100 + 1
UUGAGGUUUUUGCGUAUAUGGCACCCCAGGGCUUAAAUUAAAGUCAUCCCAAGUGCCAAACAGCUGCCUCAAGUGC-CGCACUUGAG----UGUCGCUCCUCGAA--------
((((((............((((((.....(((((......))))).......))))))...(((.((((((((((.-..))))))))----.)).))))))))).-------- ( -34.60)
>consensus
UUGAGGUUUUUAUAUAUAUGGCACCCCAGGGCUUAAAUUAAAGUCAUCCCGAGUGCCAAACAGCUGCCUCAAGUGC_CGCACUUGAGCCGAUCUCGAUCC__GAA________
..................((((((.....(((((......))))).......)))))).........((((((((....)))))))).......................... (-19.70 = -20.57 +   0.86)

alignment

secondary structure

dotplot

Window 5

Location	6,540,970 – 6,541,074
Length	104
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	78.86
Mean single sequence MFE	-34.58
Consensus MFE	-22.94
Energy contribution	-23.25
Covariance contribution	0.31
Combinations/Pair	1.19
Mean z-score	-2.14
Structure conservation index	0.66
SVM decision value	1.25
SVM RNA-class probability	0.935705
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6540970 104 - 22407834
--------UUCCGGGAUCCAGAUCGGCUCAAGUGCG-GCACUUGAGGCAGCUGUUUGGCACUCGGGAUGACUUUAAUUUAAGCCCUGGGGUGCCAUAUAUAUGGAAACCUCAA
--------....((..((((....(.((((((((..-.)))))))).)...(((.((((((((.((..(.(((......)))).)).)))))))).)))..))))..)).... ( -37.50)
>DroPse_CAF1 13670 100 - 1
--------GUCGAGGAGCGAGA----CUCAAGUGCG-GCACUUGAGGCAGCUGUUUGGCACUUGGGAUGACUUUAAUUUAAGCCCUGGGGUGCCAUAUACGCAAAAACCUCAA
--------...(((((((....----((((((((..-.))))))))...)))((.((((((((.((..(.(((......)))).)).))))))))...)).......)))).. ( -35.80)
>DroYak_CAF1 13585 111 - 1
AUUCCGGAUUCC-GGACCCAGAUCGGCUCAAGUGCG-ACACUUGAGGCAGCUGUUUGGCACUCGGGAUGACUUUAAUUUAAGCCCUGGGGUGCCAUCUAUAUCGAAACCUCAA
..(((((...))-)))..(((...(.((((((((..-.)))))))).)..)))..((((((((.((..(.(((......)))).)).)))))))).................. ( -36.00)
>DroMoj_CAF1 123447 91 - 1
-------------GGGCCAACAGGGGCUGAAGUGCGA----UUGAAGCAGCUGU-UGGCACU--UG--GAAUUUAAUUGAGGCCCAGGGGUGCCAUCUAUAUAAAAACCUCAA
-------------(((((..((((.((..((((((..----.....))).)).)-..)).))--))--...((.....))))))).(((((...............))))).. ( -27.36)
>DroAna_CAF1 13979 98 - 1
--------------GAUGAUGAUCGGCUCAAGUGCC-GCACUUGAGCCAGCUGUUUGGCACUCGGGAUGACUUUAAUUUAAGCCCUGGGGUGCCAUAUAUACGAAAACCUCAA
--------------..(((.(...((((((((((..-.))))))))))...(((.((((((((.((..(.(((......)))).)).)))))))).)))........).))). ( -34.60)
>DroPer_CAF1 13701 100 - 1
--------UUCGAGGAGCGACA----CUCAAGUGCG-GCACUUGAGGCAGCUGUUUGGCACUUGGGAUGACUUUAAUUUAAGCCCUGGGGUGCCAUAUACGCAAAAACCUCAA
--------...(((((((..(.----((((((((..-.)))))))))..)))((.((((((((.((..(.(((......)))).)).))))))))...)).......)))).. ( -36.20)
>consensus
________UUC__GGACCAAGAUCGGCUCAAGUGCG_GCACUUGAGGCAGCUGUUUGGCACUCGGGAUGACUUUAAUUUAAGCCCUGGGGUGCCAUAUAUACAAAAACCUCAA
.............((...........((((((((....)))))))).....(((.((((((((.((....(((......)))..)).))))))))...)))......)).... (-22.94 = -23.25 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:09 2006