Locus 5116

Sequence ID	3R_DroMel_CAF1
Location	13,472,360 – 13,472,492
Length	132
Max. P	0.886315

overview

Window 4

Location	13,472,360 – 13,472,457
Length	97
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	67.54
Mean single sequence MFE	-24.72
Consensus MFE	-17.90
Energy contribution	-17.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.09
Structure conservation index	0.72
SVM decision value	0.94
SVM RNA-class probability	0.886315
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13472360 97 + 27905053
-UAC--GUU-------CAAUGCCCAA-------AUAAAAAA--GAUAGUUCACUAUCGAGACUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCU
-..(--(((-------(.........-------........--(((((....))))).((...(((((((((((((.......)))))))..)))).))..))....))))).... ( -27.90)
>DroPse_CAF1 31006 100 + 1
AGAA--AAA-------AGAGGGUGUGUGUCCUG--GACAGA-----GGAUCACACGUUCCGAAUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCU
....--...-------((((.(((((((((((.--.....)-----))).)))))(((....((((((((((((((.......)))))))..)))).)))....)))..)).)))) ( -37.00)
>DroSec_CAF1 22305 99 + 1
-UAU--GUU-------CAAUACCCAA-------AUAAAAAAAAAGUAUAUAGACUUCAAGACUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCU
-...--(((-------(.........-------.........((((......))))..((...(((((((((((((.......)))))))..)))).))..))....))))..... ( -21.40)
>DroEre_CAF1 18326 84 + 1
-UAG--U------------UACGGAA-------A-AA---------AAAAUACCUUUAAGACUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCU
-...--.------------.......-------.-..---------............((...(((((((((((((.......)))))))..)))).))..)).(((....))).. ( -18.30)
>DroYak_CAF1 24373 97 + 1
-UAA--AUCAUUAUUGUACUACAUAA-------UUAA---------AAAAGUUCAAGAAGACUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCU
-...--....................-------....---------....((((....((...(((((((((((((.......)))))))..)))).))..))....))))..... ( -20.40)
>DroMoj_CAF1 23159 92 + 1
-UACAAACG-------UAAGACAUUG-------AGAA---------AAAAAAUUGUUCCUCGUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCU
-......((-------(.((.(((((-------(((.---------.........((((.....)))).(((((((.......)))))))..))))).)))))..)))........ ( -23.30)
>consensus
_UAA__AUU_______CAAUACACAA_______AUAA_________AAAAAACCAUUAAGACUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCU
................................................................((((.(((((((.......))))))).)))).....(((.....)))..... (-17.90 = -17.90 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	13,472,360 – 13,472,457
Length	97
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	67.54
Mean single sequence MFE	-26.20
Consensus MFE	-19.77
Energy contribution	-19.77
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-0.78
Structure conservation index	0.75
SVM decision value	0.55
SVM RNA-class probability	0.780118
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13472360 97 - 27905053
AGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAGUCUCGAUAGUGAACUAUC--UUUUUUAU-------UUGGGCAUUG-------AAC--GUA-
...((.(((((.......)))))((((.(((((.......))))).))))((((((...(((((....)))))--......))-------))))))....-------...--...- ( -29.20)
>DroPse_CAF1 31006 100 - 1
AGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAUUCGGAACGUGUGAUCC-----UCUGUC--CAGGACACACACCCUCU-------UUU--UUCU
.((((....)))).......((((((..(((((.......)))))....(((....)))..(((((.(((-----(.....--.)))))))))..)))))-------)..--.... ( -32.70)
>DroSec_CAF1 22305 99 - 1
AGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAGUCUUGAAGUCUAUAUACUUUUUUUUUAU-------UUGGGUAUUG-------AAC--AUA-
......(((((.......)))))((((.(((((.......))))).))))((((((...(((((......)))))......))-------))))......-------...--...- ( -23.60)
>DroEre_CAF1 18326 84 - 1
AGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAGUCUUAAAGGUAUUUU---------UU-U-------UUCCGUA------------A--CUA-
.((((....)))).((...((.(((((.(((((.......))))).))))))).........((......---------..-.-------..)))).------------.--...- ( -20.30)
>DroYak_CAF1 24373 97 - 1
AGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAGUCUUCUUGAACUUUU---------UUAA-------UUAUGUAGUACAAUAAUGAU--UUA-
.((((....)))).(((((...(((((.(((((.......))))).)))))((((....)))).......---------....-------.)))))..............--...- ( -24.00)
>DroMoj_CAF1 23159 92 - 1
AGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAACGAGGAACAAUUUUUU---------UUCU-------CAAUGUCUUA-------CGUUUGUA-
.((((....))))...((((((((.((..((((((((......)).))))))...((((((........)---------))))-------).)).)))))-------))).....- ( -27.40)
>consensus
AGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAGUCUUAAAGGUGAUUU_________UUAU_______UUAGGUAUUA_______AAU__GUA_
.((((....))))......((.(((((.(((((.......))))).)))))))............................................................... (-19.77 = -19.77 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	13,472,379 – 13,472,492
Length	113
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	79.86
Mean single sequence MFE	-31.28
Consensus MFE	-25.32
Energy contribution	-25.65
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.26
Structure conservation index	0.81
SVM decision value	0.37
SVM RNA-class probability	0.708954
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13472379 113 + 27905053
AAAAA--GAUAGUUCACUAUCGAGACUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGAGUGAUCGCGAUUU
.....--(((((....)))))((.((((((.(((((((((.......))))).....((((.(((.(((((....))).)).))).))))...)))).))))))..))....... ( -34.60)
>DroGri_CAF1 24347 90 + 1
-------------------------GUUGGAGAUGCGGGGCAUUGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCUCAUGAUCGUCGCCA
-------------------------((.((((.(((((((.......))))))).)))).)).......((((..((((........))))..(((......)))....)))).. ( -28.50)
>DroSec_CAF1 22324 115 + 1
AAAAAAAAGUAUAUAGACUUCAAGACUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGAGUGAUCGCGACUU
.......(((((..((((((((.....))))).(((((((.......)))))))..)))...)))))..((((..((((........))))..(((......))).))))..... ( -29.30)
>DroEre_CAF1 18339 106 + 1
A---------AAAAUACCUUUAAGACUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGAGUGAUCGCGGUUC
.---------.....(((....((...(((((((((((((.......)))))))..)))).))..))..((((..((((........))))..(((......))).))))))).. ( -30.50)
>DroYak_CAF1 24399 106 + 1
A---------AAAAGUUCAAGAAGACUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGAGUGAUCGAGUUUC
.---------............((((((((((.(((((((.......))))))).)))((((..(((.....)))((((........))))...........)))).))))))). ( -32.80)
>DroMoj_CAF1 23180 105 + 1
A---------AAAAAAUUGUUCCUCGUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGGGU-AUCGUCCGCG
.---------...............((.((((.(((((((.......))))))).)))).)).......(((..(((((........))))...(((....)))-...)..))). ( -32.00)
>consensus
A_________AAAAAACCAUCAAGACUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGAGUGAUCGCGAUUC
.............................(((.(((((((.......))))))).)))((((..(((.....)))((((........))))...........))))......... (-25.32 = -25.65 +   0.33)

alignment

secondary structure

dotplot

Window 7

Location	13,472,379 – 13,472,492
Length	113
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	79.86
Mean single sequence MFE	-36.40
Consensus MFE	-33.08
Energy contribution	-33.08
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.29
Structure conservation index	0.91
SVM decision value	0.42
SVM RNA-class probability	0.728695
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13472379 113 - 27905053
AAAUCGCGAUCACUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAGUCUCGAUAGUGAACUAUC--UUUUU
.......((..(((.((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))).))).))(((((....)))))--..... ( -41.50)
>DroGri_CAF1 24347 90 - 1
UGGCGACGAUCAUGAGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCAAUGCCCCGCAUCUCCAAC-------------------------
...............((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))...------------------------- ( -33.00)
>DroSec_CAF1 22324 115 - 1
AAGUCGCGAUCACUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAGUCUUGAAGUCUAUAUACUUUUUUUU
.((.(......(((.((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))).)))......).)).............. ( -35.30)
>DroEre_CAF1 18339 106 - 1
GAACCGCGAUCACUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAGUCUUAAAGGUAUUUU---------U
..(((...(..(((.((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))).)))..)...))).....---------. ( -38.10)
>DroYak_CAF1 24399 106 - 1
GAAACUCGAUCACUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAGUCUUCUUGAACUUUU---------U
.......((..(((.((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))).)))..))..........---------. ( -36.50)
>DroMoj_CAF1 23180 105 - 1
CGCGGACGAU-ACCCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAACGAGGAACAAUUUUUU---------U
...((.....-..))((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))..................---------. ( -34.00)
>consensus
AAACCGCGAUCACUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAGUCUUAAAGAUUUUUU_________U
...............((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))............................ (-33.08 = -33.08 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:41 2006