Locus 9994

Sequence ID	3R_DroMel_CAF1
Location	26,767,343 – 26,767,491
Length	148
Max. P	0.900283

overview

Window 8

Location	26,767,343 – 26,767,461
Length	118
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	74.62
Mean single sequence MFE	-32.75
Consensus MFE	-19.68
Energy contribution	-21.02
Covariance contribution	1.34
Combinations/Pair	1.21
Mean z-score	-1.40
Structure conservation index	0.60
SVM decision value	0.24
SVM RNA-class probability	0.648162
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26767343 118 + 27905053
AAAAGAAAGUAUUCAACAUAAGGGCAGUUAAGGUAUUCCAGUUUGACAUCGACUGCAGGACUCGCGGCCAGUUUAUCCUGCUGUGGACGUUGCAAACAGCAAACAUGCCGCAGUCCUG
.......................((((((..((....)).(.....)...))))))((((((.(((((..((((.(((......))).((((....))))))))..))))))))))). ( -34.70)
>DroSec_CAF1 71105 118 + 1
AAAAGAAAGUAUUCAACAUAAGGGCAGUUAAGGUAUUCCACUUUGGCAUCGACUGCAGGACUCGCGGCCAGUUUAUCCUGCUGUGGACGUUGCAAACAGCAAACAUGCCGCAGUCCUG
.......................((((((..(((...((.....)).)))))))))((((((.(((((..((((.(((......))).((((....))))))))..))))))))))). ( -35.20)
>DroSim_CAF1 74775 117 + 1
AAAAGAAUGUAUUCAGCA-AAGGGCAGUUAAGGUAUUCCACUUUGGCAUCGACUGCAGGACUCGCGGCCAGUUUAUCCUGCUGUGGACGUUGCAAACAGCAAACAUGCCGCAGUCCUG
........(((.((.((.-....)).((((((((.....))))))))...)).)))((((((.(((((..((((.(((......))).((((....))))))))..))))))))))). ( -37.50)
>DroEre_CAF1 72432 118 + 1
AAAAGCACUUCUCCAGCAAAGGGAAAGUUAAGGUAUUUCCGCUUGGCUUCGAUUCCAGGACUCGCGGCCAGUUUAUCCUGCUGUGGACGUUGCAAACAGCAAACAUGCCGCAGUCCUG
..((((((((..((......))..))))...((.....))))))...........(((((((.(((((..((((.(((......))).((((....))))))))..)))))))))))) ( -39.60)
>DroYak_CAF1 73799 113 + 1
-CAAGCACUUCUCUAAUAA----GAAGUUAAGGUAUUUCGGUUUAGCUUCGAUUCCAGGACUCGCGGUCAGUUUUUACUGCUGCGGACGUUGCAAACAGCAAACAUGCCGCAGUCCUG
-..................----(((((((((.(.....).))))))))).....((((((((((((.((((....))))))))((...((((.....)))).....))).))))))) ( -34.70)
>DroAna_CAF1 81601 90 + 1
-------------UAAUGU----CUUAUUAAGGCAUUUUGAAUUCGAUCUGUUCCC----UUCAUUUUCAGUUUAUCCUUGUGUGGACGUUGCAA-------ACACGCCACAGUCCUG
-------------((((((----((...(((((....(((((...((.........----.))...))))).....)))))...))))))))...-------................ ( -14.80)
>consensus
AAAAGAAAGUAUUCAACAUAAGGGCAGUUAAGGUAUUCCAGUUUGGCAUCGACUCCAGGACUCGCGGCCAGUUUAUCCUGCUGUGGACGUUGCAAACAGCAAACAUGCCGCAGUCCUG
..........................((((((.........))))))........(((((((.(((((..((((((......))))))(((((.....)).)))..)))))))))))) (-19.68 = -21.02 +   1.34)

alignment

secondary structure

dotplot

Window 9

Location	26,767,343 – 26,767,461
Length	118
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	74.62
Mean single sequence MFE	-32.78
Consensus MFE	-19.59
Energy contribution	-21.20
Covariance contribution	1.61
Combinations/Pair	1.14
Mean z-score	-1.30
Structure conservation index	0.60
SVM decision value	-0.03
SVM RNA-class probability	0.518742
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26767343 118 - 27905053
CAGGACUGCGGCAUGUUUGCUGUUUGCAACGUCCACAGCAGGAUAAACUGGCCGCGAGUCCUGCAGUCGAUGUCAAACUGGAAUACCUUAACUGCCCUUAUGUUGAAUACUUUCUUUU
.(((((((((((....((((.....)))).((((......))))......))))).))))))(((((..(.((...........)).)..)))))....................... ( -32.80)
>DroSec_CAF1 71105 118 - 1
CAGGACUGCGGCAUGUUUGCUGUUUGCAACGUCCACAGCAGGAUAAACUGGCCGCGAGUCCUGCAGUCGAUGCCAAAGUGGAAUACCUUAACUGCCCUUAUGUUGAAUACUUUCUUUU
.(((((((((((....((((.....)))).((((......))))......))))).))))))(((((..(..((.....))......)..)))))....................... ( -33.90)
>DroSim_CAF1 74775 117 - 1
CAGGACUGCGGCAUGUUUGCUGUUUGCAACGUCCACAGCAGGAUAAACUGGCCGCGAGUCCUGCAGUCGAUGCCAAAGUGGAAUACCUUAACUGCCCUU-UGCUGAAUACAUUCUUUU
((((((((((((....((((.....)))).((((......))))......))))).)))))))(((.(((.((......((....))......))...)-)))))............. ( -34.50)
>DroEre_CAF1 72432 118 - 1
CAGGACUGCGGCAUGUUUGCUGUUUGCAACGUCCACAGCAGGAUAAACUGGCCGCGAGUCCUGGAAUCGAAGCCAAGCGGAAAUACCUUAACUUUCCCUUUGCUGGAGAAGUGCUUUU
((((((((((((....((((.....)))).((((......))))......))))).))))))).....(((((.....((.....))...((((..((......))..))))))))). ( -40.80)
>DroYak_CAF1 73799 113 - 1
CAGGACUGCGGCAUGUUUGCUGUUUGCAACGUCCGCAGCAGUAAAAACUGACCGCGAGUCCUGGAAUCGAAGCUAAACCGAAAUACCUUAACUUC----UUAUUAGAGAAGUGCUUG-
(((((((((((((..(((((((((.((.......)))))))))))...)).)))).)))))))......((((......(......)...(((((----((....))))))))))).- ( -39.50)
>DroAna_CAF1 81601 90 - 1
CAGGACUGUGGCGUGU-------UUGCAACGUCCACACAAGGAUAAACUGAAAAUGAA----GGGAACAGAUCGAAUUCAAAAUGCCUUAAUAAG----ACAUUA-------------
..((((.((.(((...-------.))).))))))....((((......((((..(((.----(....)...)))..)))).....))))......----......------------- ( -15.20)
>consensus
CAGGACUGCGGCAUGUUUGCUGUUUGCAACGUCCACAGCAGGAUAAACUGGCCGCGAGUCCUGCAAUCGAAGCCAAACUGAAAUACCUUAACUGCCCUUAUGUUGAAUACGUUCUUUU
(((((((((((((((((.((.....)))))))......(((......)))))))).)))))))....................................................... (-19.59 = -21.20 +   1.61)

alignment

secondary structure

dotplot

Window 0

Location	26,767,383 – 26,767,491
Length	108
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	78.31
Mean single sequence MFE	-34.26
Consensus MFE	-21.07
Energy contribution	-23.93
Covariance contribution	2.86
Combinations/Pair	1.09
Mean z-score	-1.48
Structure conservation index	0.62
SVM decision value	0.16
SVM RNA-class probability	0.613247
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26767383 108 + 27905053
GUUUGACAUCGACUGCAGGACUCGCGGCCAGUUUAUCCUGCUGUGGACGUUGCAAACAGCAAACAUGCCGCAGUCCUGUUCCUGCCAGCCACUCCGGCUCCUCUUUGG-------
......((..((..((((((((.(((((..((((.(((......))).((((....))))))))..))))))))))))).......((((.....))))..))..)).------- ( -36.00)
>DroSec_CAF1 71145 108 + 1
CUUUGGCAUCGACUGCAGGACUCGCGGCCAGUUUAUCCUGCUGUGGACGUUGCAAACAGCAAACAUGCCGCAGUCCUGUUCCUGCCAGCCACUCCGGCUCCUCUUCGG-------
...(((((..((..((((((((.(((((..((((.(((......))).((((....))))))))..))))))))))))))).)))))(((.....)))..........------- ( -42.10)
>DroSim_CAF1 74814 108 + 1
CUUUGGCAUCGACUGCAGGACUCGCGGCCAGUUUAUCCUGCUGUGGACGUUGCAAACAGCAAACAUGCCGCAGUCCUGUUCCUGCCAGCCACUCCGGCUCCACUUUGG-------
...(((((..((..((((((((.(((((..((((.(((......))).((((....))))))))..))))))))))))))).)))))(((.....)))..........------- ( -42.10)
>DroEre_CAF1 72472 108 + 1
GCUUGGCUUCGAUUCCAGGACUCGCGGCCAGUUUAUCCUGCUGUGGACGUUGCAAACAGCAAACAUGCCGCAGUCCUGUUCCUGCCAGCCACUCCGGCUCCUCUGUGU-------
...((((...((...(((((((.(((((..((((.(((......))).((((....))))))))..)))))))))))).))..))))(((.....)))..........------- ( -39.70)
>DroYak_CAF1 73834 106 + 1
GUUUAGCUUCGAUUCCAGGACUCGCGGUCAGUUUUUACUGCUGCGGACGUUGCAAACAGCAAACAUGCCGCAGUCCUGUUCCUGCCAGCCACU--AGCCACUCCGGCU-------
.....((...((...((((((((((((.((((....))))))))((...((((.....)))).....))).))))))).))..))........--((((.....))))------- ( -33.00)
>DroAna_CAF1 81624 104 + 1
AAUUCGAUCUGUUCCC----UUCAUUUUCAGUUUAUCCUUGUGUGGACGUUGCAA-------ACACGCCACAGUCCUGUUACCGCCUGCCCCGCCCACUUCACCGCGCACUGCCA
................----........((((..........((((.((..(((.-------...((..(((....)))...))..)))..)).))))..........))))... ( -12.65)
>consensus
GUUUGGCAUCGACUCCAGGACUCGCGGCCAGUUUAUCCUGCUGUGGACGUUGCAAACAGCAAACAUGCCGCAGUCCUGUUCCUGCCAGCCACUCCGGCUCCUCUGUGG_______
...((((...((...(((((((.(((((..((((((......))))))(((((.....)).)))..)))))))))))).))..))))(((.....)))................. (-21.07 = -23.93 +   2.86)

alignment

secondary structure

dotplot

Window 1

Location	26,767,383 – 26,767,491
Length	108
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	78.31
Mean single sequence MFE	-40.17
Consensus MFE	-26.22
Energy contribution	-27.62
Covariance contribution	1.40
Combinations/Pair	1.29
Mean z-score	-1.87
Structure conservation index	0.65
SVM decision value	1.01
SVM RNA-class probability	0.900283
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26767383 108 - 27905053
-------CCAAAGAGGAGCCGGAGUGGCUGGCAGGAACAGGACUGCGGCAUGUUUGCUGUUUGCAACGUCCACAGCAGGAUAAACUGGCCGCGAGUCCUGCAGUCGAUGUCAAAC
-------((.....))((((.....))))((((.((.((((((((((((....((((.....)))).((((......))))......))))).)))))))...))..)))).... ( -40.30)
>DroSec_CAF1 71145 108 - 1
-------CCGAAGAGGAGCCGGAGUGGCUGGCAGGAACAGGACUGCGGCAUGUUUGCUGUUUGCAACGUCCACAGCAGGAUAAACUGGCCGCGAGUCCUGCAGUCGAUGCCAAAG
-------((.....))((((.....))))((((.((.((((((((((((....((((.....)))).((((......))))......))))).)))))))...))..)))).... ( -43.70)
>DroSim_CAF1 74814 108 - 1
-------CCAAAGUGGAGCCGGAGUGGCUGGCAGGAACAGGACUGCGGCAUGUUUGCUGUUUGCAACGUCCACAGCAGGAUAAACUGGCCGCGAGUCCUGCAGUCGAUGCCAAAG
-------((.....))((((.....))))((((.((.((((((((((((....((((.....)))).((((......))))......))))).)))))))...))..)))).... ( -43.30)
>DroEre_CAF1 72472 108 - 1
-------ACACAGAGGAGCCGGAGUGGCUGGCAGGAACAGGACUGCGGCAUGUUUGCUGUUUGCAACGUCCACAGCAGGAUAAACUGGCCGCGAGUCCUGGAAUCGAAGCCAAGC
-------.......((.(((((.....))))).....((((((((((((....((((.....)))).((((......))))......))))).))))))).........)).... ( -40.30)
>DroYak_CAF1 73834 106 - 1
-------AGCCGGAGUGGCU--AGUGGCUGGCAGGAACAGGACUGCGGCAUGUUUGCUGUUUGCAACGUCCGCAGCAGUAAAAACUGACCGCGAGUCCUGGAAUCGAAGCUAAAC
-------((((.....))))--..(((((....((..(((((((((((((..(((((((((.((.......)))))))))))...)).)))).)))))))...))..)))))... ( -42.30)
>DroAna_CAF1 81624 104 - 1
UGGCAGUGCGCGGUGAAGUGGGCGGGGCAGGCGGUAACAGGACUGUGGCGUGU-------UUGCAACGUCCACACAAGGAUAAACUGAAAAUGAA----GGGAACAGAUCGAAUU
...((((...(..((..(((((((..(((((((((.(((....))).)).)))-------))))..))))))).))..)....))))........----(....).......... ( -31.10)
>consensus
_______CCAAAGAGGAGCCGGAGUGGCUGGCAGGAACAGGACUGCGGCAUGUUUGCUGUUUGCAACGUCCACAGCAGGAUAAACUGGCCGCGAGUCCUGCAAUCGAAGCCAAAC
................((((.....))))(((.((..(((((((((((((((((.((.....)))))))......(((......)))))))).)))))))...))...))).... (-26.22 = -27.62 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:46:37 2006