Locus 5102

Sequence ID	3R_DroMel_CAF1
Location	13,445,443 – 13,445,572
Length	129
Max. P	0.925715

overview

Window 7

Location	13,445,443 – 13,445,556
Length	113
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.15
Mean single sequence MFE	-35.70
Consensus MFE	-32.93
Energy contribution	-32.93
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.25
Structure conservation index	0.92
SVM decision value	0.64
SVM RNA-class probability	0.807052
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13445443 113 + 27905053
UGACCGCUU---GAUAUAAGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGGAAU---AAGUCUUAUAUUUU-CUUUU
.........---.....(((..((((((((((........))))....(((((...(.((.(((((.(((((.......))))).))))))).)..)---))))..))))))..-))).. ( -34.10)
>DroGri_CAF1 1666 117 + 1
AACACAUCU---CGUAUAUGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCAAUGCCCCGCAUCUCCAGUUGUUCGAAAUUAUAUUUUUGGCUUUU
........(---((....(((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))))......)))................... ( -36.00)
>DroSec_CAF1 472 116 + 1
UGACCAUUU---GACAUAAGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGAUCUCAAUAGUCUUAUUUUUU-CUUUU
.(((...((---((.((..((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))..)).))))..))).........-..... ( -38.40)
>DroWil_CAF1 3924 113 + 1
UGCUAGCUGAAUACCACAAGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGGAUU---AGAU-UUC--UUUU-AUUUU
...................((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))((((..---....-)))--)...-..... ( -33.50)
>DroYak_CAF1 1379 106 + 1
UGCCUAUUG---AACACAAGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGCUCUU----------UGUUUA-UUUUU
.......((---((((...((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))).......----------))))))-..... ( -33.70)
>DroMoj_CAF1 1473 106 + 1
AACGCCCGU---CUUGCAUGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAUG----GGAAUUAA-------UCUUUU
....(((((---......(((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))))))----))......-------...... ( -38.50)
>consensus
UGCCCACUU___AACACAAGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGGUCU___AAAU_UUAU_UUUU_CUUUU
...................((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))............................. (-32.93 = -32.93 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	13,445,443 – 13,445,556
Length	113
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.15
Mean single sequence MFE	-30.58
Consensus MFE	-23.70
Energy contribution	-23.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.69
Structure conservation index	0.77
SVM decision value	1.17
SVM RNA-class probability	0.925715
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13445443 113 - 27905053
AAAAG-AAAAUAUAAGACUU---AUUCCUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCUUAUAUC---AAGCGGUCA
.....-...(((((((....---......((((.(((((((.......))))))).)))).....(((.....)))((((........))))........))))))).---......... ( -27.80)
>DroGri_CAF1 1666 117 - 1
AAAAGCCAAAAAUAUAAUUUCGAACAACUGGAGAUGCGGGGCAUUGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCAUAUACG---AGAUGUGUU
..........((((((.(((((.......((((.(((((((.......))))))).)))).....(((.....)))((((........))))..............))---))))))))) ( -29.80)
>DroSec_CAF1 472 116 - 1
AAAAG-AAAAAAUAAGACUAUUGAGAUCUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCUUAUGUC---AAAUGGUCA
.....-.........(((((((((.((..((.(((((((((.......))))).....((((.(((.(((((....))).)).))).))))...)))).))..)).))---.))))))). ( -33.30)
>DroWil_CAF1 3924 113 - 1
AAAAU-AAAA--GAA-AUCU---AAUCCUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCUUGUGGUAUUCAGCUAGCA
.....-....--...-....---......((((.(((((((.......))))))).))))....((((((((....))).......((((((((((......))))))..)))).))))) ( -30.90)
>DroYak_CAF1 1379 106 - 1
AAAAA-UAAACA----------AAGAGCUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCUUGUGUU---CAAUAGGCA
.....-......----------.(((((.((((.(((((((.......))))))).)))).....(((.....)))))))).((...(((((.(((......))))))---))...)).. ( -32.70)
>DroMoj_CAF1 1473 106 - 1
AAAAGA-------UUAAUUCC----CAUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCAUGCAAG---ACGGGCGUU
......-------..(((.((----(...((((.(((((((.......))))))).))))....(((...(.((..((((........))))....)).)...)))..---..))).))) ( -29.00)
>consensus
AAAAG_AAAA_AUAA_AUUU___AGAACUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCUUAUAUC___AAAUGGGCA
.............................((((.(((((((.......))))))).)))).....(((.....)))((((........))))............................ (-23.70 = -23.70 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	13,445,480 – 13,445,572
Length	92
Sequences	4
Columns	97
Reading direction	forward
Mean pairwise identity	75.00
Mean single sequence MFE	-24.20
Consensus MFE	-19.50
Energy contribution	-19.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.11
Structure conservation index	0.81
SVM decision value	0.04
SVM RNA-class probability	0.555377
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13445480 92 + 27905053
GAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGGAAU---AAGUCUUAUAUUUU-CUUUUUCCCAAACAAAUG-UUU
((((....))))(((((.((.(((((.(((((.......))))).)))))..((((.---(((...........-))).))))....)).)))-)). ( -25.90)
>DroSec_CAF1 509 93 + 1
GAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGAUCUCAAUAGUCUUAUUUUUU-CUUUUU--CAAACAAAUG-UUU
((((....))))(((((.((.(((((.(((((.......))))).))))).((((.......))))........-......--....)).)))-)). ( -22.00)
>DroYak_CAF1 1416 86 + 1
GAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGCUCUU----------UGUUUA-UUUUUUCGCUAUUGAAUGGUAU
(((((((.....)))...((.(((((.(((((.......))))).)))))))))))..----------......-.......(((((...))))).. ( -25.40)
>DroMoj_CAF1 1510 81 + 1
GAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAUG----GGAAUUAA-------UCUUUUG--CUAAUG--UA-UUU
((((....)))).(((((..((((((.(((((.......)))))....(((....----)))....)-------)))))..--)..)))--).-... ( -23.50)
>consensus
GAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGAUCU____AGUCUU_U_UUUU_CUUUUU__CAAACAAAUG_UUU
((((....))))......((.(((((.(((((.......))))).)))))))............................................. (-19.50 = -19.50 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	13,445,480 – 13,445,572
Length	92
Sequences	4
Columns	97
Reading direction	reverse
Mean pairwise identity	75.00
Mean single sequence MFE	-22.43
Consensus MFE	-17.90
Energy contribution	-17.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.45
Structure conservation index	0.80
SVM decision value	0.77
SVM RNA-class probability	0.845751
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13445480 92 - 27905053
AAA-CAUUUGUUUGGGAAAAAG-AAAAUAUAAGACUU---AUUCCUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUC
...-..((((((((((((.(((-...........)))---.)))))((((.(((((((.......))))))).))))........)))))))..... ( -24.00)
>DroSec_CAF1 509 93 - 1
AAA-CAUUUGUUUG--AAAAAG-AAAAAAUAAGACUAUUGAGAUCUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUC
...-..((((((((--......-........(((((....)).)))((((.(((((((.......))))))).)))).......))))))))..... ( -20.60)
>DroYak_CAF1 1416 86 - 1
AUACCAUUCAAUAGCGAAAAAA-UAAACA----------AAGAGCUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUC
......................-......----------..((((.((((.(((((((.......))))))).)))).....(((.....))))))) ( -22.90)
>DroMoj_CAF1 1510 81 - 1
AAA-UA--CAUUAG--CAAAAGA-------UUAAUUCC----CAUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUC
...-..--..((((--((...((-------.....)).----....((((.(((((((.......))))))).))))....))))))((....)).. ( -22.20)
>consensus
AAA_CAUUCAUUAG__AAAAAG_AAAA_A_AAGACU____AGAACUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUC
..............................................((((.(((((((.......))))))).)))).....(((.....))).... (-17.90 = -17.90 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:16 2006