Locus 1027

Sequence ID	2L_DroMel_CAF1
Location	2,912,391 – 2,912,551
Length	160
Max. P	0.993289

overview

Window 6

Location	2,912,391 – 2,912,511
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.50
Mean single sequence MFE	-25.98
Consensus MFE	-21.80
Energy contribution	-22.24
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-2.46
Structure conservation index	0.84
SVM decision value	2.39
SVM RNA-class probability	0.993289
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2912391 120 + 22407834
UUUCAUUUGUAAUCGUUUUUGCAAUUGUAUUCAAUUGUUGUGACAUUUUAAUUGCUCGCAAUGUAAGCGCUGUAAGCAUAAAUUACGUAAUUAAUUUAUGCUGUACAACUUUUAAUCUUU
..............((.((((((((((....)))))(((((((((.......)).)))))))))))).))(((((((((((((((......))))))))))).))))............. ( -25.60)
>DroSec_CAF1 30879 120 + 1
UUUCAGUUGUAAUCAUUUUUGCAAUUGUAUUCAAUUGUUGUGACAUUUUAAUUGAUCGCAAUGUAAGCGCUGUAAGCAUAAAUUACGUUAUUAAUUUAUGCUGUACGACUUUUAAGCUUU
....(((((((......((((((.((((..(((((((...........)))))))..)))))))))).......(((((((((((......))))))))))).))))))).......... ( -28.00)
>DroSim_CAF1 31475 120 + 1
UUUCAGUUGUAAUCAUUUUUGCAAUUGUAUUCAAUUGUUGUGACAUUUUAAUUGCUCGCAAUGUAAGCGCUGUAAGCAUAAAUUACGUUAUUAAUUUAUGCUGUACGACUUUUAAGCUUU
....(((((((.((((....(((((((....))))))).)))).........(((.(((.......)))..)))(((((((((((......))))))))))).))))))).......... ( -28.60)
>DroEre_CAF1 31666 120 + 1
UUUCAUUUGUAAUCAUUUUUGCAAUUGUAUUCAAUUGUUGUGACAUUUUAAUUGCUCGCAAUGUAAGCGCUGUAAGCAUAAAUUACGUAAUUAUUUUAUCCUCUACGACUUUUAAUCGUU
........((((((((....(((((((....))))))).)))).........((((..((.((....)).))..))))....))))..................((((.......)))). ( -19.10)
>DroYak_CAF1 31853 120 + 1
UUUCAUUUGUAAUCAUUUUUGCAAUUGUAUUCAAUUGUUGUGACAUUUUAAUUGCUCGCAAUGUAAGCGCUGCAAGCAUAAAUUACGUAAUUAAUUUAUGCUGUACGGCUUUUAAUCUUU
...((.((((((......)))))).)).........(((((((((.......)).))))))).((((.((((..(((((((((((......)))))))))))...)))).))))...... ( -28.60)
>consensus
UUUCAUUUGUAAUCAUUUUUGCAAUUGUAUUCAAUUGUUGUGACAUUUUAAUUGCUCGCAAUGUAAGCGCUGUAAGCAUAAAUUACGUAAUUAAUUUAUGCUGUACGACUUUUAAUCUUU
...((.((((((......)))))).)).........(((((((((.......)).))))))).((((.(.(((((((((((((((......))))))))))).)))).).))))...... (-21.80 = -22.24 +   0.44)

alignment

secondary structure

dotplot

Window 7

Location	2,912,391 – 2,912,511
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.50
Mean single sequence MFE	-22.26
Consensus MFE	-18.38
Energy contribution	-18.46
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-2.63
Structure conservation index	0.83
SVM decision value	2.32
SVM RNA-class probability	0.992320
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2912391 120 - 22407834
AAAGAUUAAAAGUUGUACAGCAUAAAUUAAUUACGUAAUUUAUGCUUACAGCGCUUACAUUGCGAGCAAUUAAAAUGUCACAACAAUUGAAUACAAUUGCAAAAACGAUUACAAAUGAAA
...(((.....((((((.(((((((((((......)))))))))))))))))((((.......)))).........)))....((((((....))))))..................... ( -25.30)
>DroSec_CAF1 30879 120 - 1
AAAGCUUAAAAGUCGUACAGCAUAAAUUAAUAACGUAAUUUAUGCUUACAGCGCUUACAUUGCGAUCAAUUAAAAUGUCACAACAAUUGAAUACAAUUGCAAAAAUGAUUACAACUGAAA
.((((......((.(((.(((((((((((......)))))))))))))).)))))).(((((..((((.......((...)).((((((....))))))......))))..))).))... ( -21.50)
>DroSim_CAF1 31475 120 - 1
AAAGCUUAAAAGUCGUACAGCAUAAAUUAAUAACGUAAUUUAUGCUUACAGCGCUUACAUUGCGAGCAAUUAAAAUGUCACAACAAUUGAAUACAAUUGCAAAAAUGAUUACAACUGAAA
...((((....((.(((.(((((((((((......)))))))))))))).))((.......)))))).........((((...((((((....))))))......))))........... ( -23.70)
>DroEre_CAF1 31666 120 - 1
AACGAUUAAAAGUCGUAGAGGAUAAAAUAAUUACGUAAUUUAUGCUUACAGCGCUUACAUUGCGAGCAAUUAAAAUGUCACAACAAUUGAAUACAAUUGCAAAAAUGAUUACAAAUGAAA
.(((((.....)))))...........((((((((((((.((.((.......)).)).)))))).((((((......(((.......)))....)))))).....))))))......... ( -17.70)
>DroYak_CAF1 31853 120 - 1
AAAGAUUAAAAGCCGUACAGCAUAAAUUAAUUACGUAAUUUAUGCUUGCAGCGCUUACAUUGCGAGCAAUUAAAAUGUCACAACAAUUGAAUACAAUUGCAAAAAUGAUUACAAAUGAAA
...(((.....((.(((.(((((((((((......)))))))))))))).))((((.......)))).........)))....((((((....))))))..................... ( -23.10)
>consensus
AAAGAUUAAAAGUCGUACAGCAUAAAUUAAUUACGUAAUUUAUGCUUACAGCGCUUACAUUGCGAGCAAUUAAAAUGUCACAACAAUUGAAUACAAUUGCAAAAAUGAUUACAAAUGAAA
...........((.(((.(((((((((((......)))))))))))))).))....(((((..((....))..))))).....((((((....))))))..................... (-18.38 = -18.46 +   0.08)

alignment

secondary structure

dotplot

Window 8

Location	2,912,431 – 2,912,551
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.92
Mean single sequence MFE	-24.62
Consensus MFE	-19.26
Energy contribution	-19.94
Covariance contribution	0.68
Combinations/Pair	1.06
Mean z-score	-1.56
Structure conservation index	0.78
SVM decision value	0.13
SVM RNA-class probability	0.596430
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2912431 120 + 22407834
UGACAUUUUAAUUGCUCGCAAUGUAAGCGCUGUAAGCAUAAAUUACGUAAUUAAUUUAUGCUGUACAACUUUUAAUCUUUAUUUCACAGUAAAUAACUUGCAUCGGUCAUUUAAGUGGAA
...(((((.(((.((.((..(((((((...(((((((((((((((......))))))))))).))))..........(((((......)))))...))))))))))).))).)))))... ( -25.30)
>DroSec_CAF1 30919 117 + 1
UGACAUUUUAAUUGAUCGCAAUGUAAGCGCUGUAAGCAUAAAUUACGUUAUUAAUUUAUGCUGUACGACUUUUAAGCUUUAUUUCACAGUAA---ACUUGCAUCGGUCAUUUAAGUGGAA
...(((((....((((((..(((((((.(((((.(((((((((((......)))))))))))....(.((....)))........)))))..---.)))))))))))))...)))))... ( -30.00)
>DroSim_CAF1 31515 120 + 1
UGACAUUUUAAUUGCUCGCAAUGUAAGCGCUGUAAGCAUAAAUUACGUUAUUAAUUUAUGCUGUACGACUUUUAAGCUUUAUUUCACAGUAAAUAACUUGCAUCGGUCAUUUAAGUGGAA
...(((((.(((.((.((..(((((((...(((((((((((((((......))))))))))).))))..........(((((......)))))...))))))))))).))).)))))... ( -24.60)
>DroEre_CAF1 31706 120 + 1
UGACAUUUUAAUUGCUCGCAAUGUAAGCGCUGUAAGCAUAAAUUACGUAAUUAUUUUAUCCUCUACGACUUUUAAUCGUUAUUCCAUAGUAAAUAACUUGCAUUGGUCAUUUAACUGAAA
((((........((((..((.((....)).))..))))........((((((((((........((((.......))))...........)))))).))))....))))........... ( -17.01)
>DroYak_CAF1 31893 120 + 1
UGACAUUUUAAUUGCUCGCAAUGUAAGCGCUGCAAGCAUAAAUUACGUAAUUAAUUUAUGCUGUACGGCUUUUAAUCUUUAUUAUACAGUAAAUAACUUGCAUCGGUCAUUUAACUGGAA
((((......((((....))))(((((.((((..(((((((((((......)))))))))))...))))........((((((....))))))...)))))....))))........... ( -26.20)
>consensus
UGACAUUUUAAUUGCUCGCAAUGUAAGCGCUGUAAGCAUAAAUUACGUAAUUAAUUUAUGCUGUACGACUUUUAAUCUUUAUUUCACAGUAAAUAACUUGCAUCGGUCAUUUAAGUGGAA
...(((((....((.(((..(((((((...(((((((((((((((......))))))))))).))))...........((((......))))....)))))))))).))...)))))... (-19.26 = -19.94 +   0.68)

alignment

secondary structure

dotplot

Window 9

Location	2,912,431 – 2,912,551
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.92
Mean single sequence MFE	-25.92
Consensus MFE	-18.40
Energy contribution	-19.00
Covariance contribution	0.60
Combinations/Pair	1.11
Mean z-score	-2.43
Structure conservation index	0.71
SVM decision value	0.10
SVM RNA-class probability	0.582986
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2912431 120 - 22407834
UUCCACUUAAAUGACCGAUGCAAGUUAUUUACUGUGAAAUAAAGAUUAAAAGUUGUACAGCAUAAAUUAAUUACGUAAUUUAUGCUUACAGCGCUUACAUUGCGAGCAAUUAAAAUGUCA
...(((.((((((((........))))))))..))).......(((.....((((((.(((((((((((......)))))))))))))))))((((.......)))).........))). ( -29.50)
>DroSec_CAF1 30919 117 - 1
UUCCACUUAAAUGACCGAUGCAAGU---UUACUGUGAAAUAAAGCUUAAAAGUCGUACAGCAUAAAUUAAUAACGUAAUUUAUGCUUACAGCGCUUACAUUGCGAUCAAUUAAAAUGUCA
......((((.(((((((((.((((---...((((((..((..(((....)))..))..((((((((((......)))))))))))))))).)))).))))).).))).))))....... ( -24.70)
>DroSim_CAF1 31515 120 - 1
UUCCACUUAAAUGACCGAUGCAAGUUAUUUACUGUGAAAUAAAGCUUAAAAGUCGUACAGCAUAAAUUAAUAACGUAAUUUAUGCUUACAGCGCUUACAUUGCGAGCAAUUAAAAUGUCA
...(((.((((((((........))))))))..))).......((((....((.(((.(((((((((((......)))))))))))))).))((.......))))))............. ( -27.70)
>DroEre_CAF1 31706 120 - 1
UUUCAGUUAAAUGACCAAUGCAAGUUAUUUACUAUGGAAUAACGAUUAAAAGUCGUAGAGGAUAAAAUAAUUACGUAAUUUAUGCUUACAGCGCUUACAUUGCGAGCAAUUAAAAUGUCA
(((((..((((((((........))))))))...)))))..(((((.....)))))....((((...(((((.((((((.((.((.......)).)).))))))...)))))...)))). ( -20.50)
>DroYak_CAF1 31893 120 - 1
UUCCAGUUAAAUGACCGAUGCAAGUUAUUUACUGUAUAAUAAAGAUUAAAAGCCGUACAGCAUAAAUUAAUUACGUAAUUUAUGCUUGCAGCGCUUACAUUGCGAGCAAUUAAAAUGUCA
...((((.(((((((........))))))))))).........(((.....((.(((.(((((((((((......)))))))))))))).))((((.......)))).........))). ( -27.20)
>consensus
UUCCACUUAAAUGACCGAUGCAAGUUAUUUACUGUGAAAUAAAGAUUAAAAGUCGUACAGCAUAAAUUAAUUACGUAAUUUAUGCUUACAGCGCUUACAUUGCGAGCAAUUAAAAUGUCA
......((((.((..(((((.(((((((((......)))))..........((.(((.(((((((((((......)))))))))))))).)))))).)))))....)).))))....... (-18.40 = -19.00 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:25 2006