Locus 1517

Sequence ID	X_DroMel_CAF1
Location	4,434,252 – 4,434,530
Length	278
Max. P	0.999990

overview

Window 8

Location	4,434,252 – 4,434,370
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.01
Mean single sequence MFE	-37.00
Consensus MFE	-31.07
Energy contribution	-31.87
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.88
Structure conservation index	0.84
SVM decision value	1.56
SVM RNA-class probability	0.963768
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4434252 118 + 22224390
UGGGAU--AUGGGUUUUGUGGUAUUAGAUCUAUGAUCUGGGAUGGGUAAUAUCAUUUGGUGGGUGUGAGGGGCUGGGGAGGUAGAUACCUGCGGGCGCGGAUGUUGCGACCCUUUUCCCA
.((((.--..(((((........(((((((...))))))).....((((((((..((.(..(((((.....(((.....)))..)))))..).))....)))))))))))))...)))). ( -38.20)
>DroSec_CAF1 36656 120 + 1
UGGGAUAUAUGGGUUUUGUGGUAUUAGAUCUAUGAUCUGGGAUGGGUAAUAACAUUUGGUGGGUGUGAGGGGCAGGGGAGGAAGAUACCUGCGGGCGCGGAUGUUGCGACCCUUUUCCCA
..((((.(((((((((.........)))))))))))))((((.((((..(((((((.......((((....(((((...........)))))...)))))))))))..))))...)))). ( -37.51)
>DroSim_CAF1 38025 120 + 1
UGGGAUAUAUGGGUUUUGUGGUAUUAGAUCUAUGAUCUGGGAUGGGUAAUAACAUUUGGUGGGUGUGAGGGGCAGGGGAGGAAGAUACCUGCGGGCGCGGAUGUUGCGACCCUUUUCCCA
..((((.(((((((((.........)))))))))))))((((.((((..(((((((.......((((....(((((...........)))))...)))))))))))..))))...)))). ( -37.51)
>DroEre_CAF1 37640 113 + 1
UGGGAU--AUGGGUUUUGUGGUAUUAGAUCUAUGAUCUGGGAUGGGUAAUAUCAUAUAGUGGGUGUGAGGAACAG-----GGAGAUACCUGCGGGCGCGGAUGUUGCGACCCUUUUCCCA
.((((.--..(((((........(((((((...))))))).....((((((((.....(..(((((.........-----....)))))..).......)))))))))))))...)))). ( -35.92)
>DroYak_CAF1 36740 113 + 1
UGGGAU--AUGGGUUUUGUGGUAUUAGAUCUAUGAUCUGGGAUGGGUAAUAUCAUUUUGUGGGUGGGAGAAAAAG-----GGAGAUACCUGCGGGCGCGGAUGUUGCGACCCUUUUCCCA
.((((.--..(((((........(((((((...))))))).....((((((((..((((..((((..........-----.....))))..))))....)))))))))))))...)))). ( -35.86)
>consensus
UGGGAU__AUGGGUUUUGUGGUAUUAGAUCUAUGAUCUGGGAUGGGUAAUAUCAUUUGGUGGGUGUGAGGGGCAGGGGAGGAAGAUACCUGCGGGCGCGGAUGUUGCGACCCUUUUCCCA
.((((.....(((((........(((((((...))))))).....((((((((..((.(..(((((..................)))))..).))....)))))))))))))...)))). (-31.07 = -31.87 +   0.80)

alignment

secondary structure

dotplot

Window 9

Location	4,434,252 – 4,434,370
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.01
Mean single sequence MFE	-24.30
Consensus MFE	-22.88
Energy contribution	-22.88
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-3.48
Structure conservation index	0.94
SVM decision value	5.56
SVM RNA-class probability	0.999990
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4434252 118 - 22224390
UGGGAAAAGGGUCGCAACAUCCGCGCCCGCAGGUAUCUACCUCCCCAGCCCCUCACACCCACCAAAUGAUAUUACCCAUCCCAGAUCAUAGAUCUAAUACCACAAAACCCAU--AUCCCA
.((((...(((.(((.......))))))...(((((.............................(((........)))...(((((...))))).)))))...........--.)))). ( -23.10)
>DroSec_CAF1 36656 120 - 1
UGGGAAAAGGGUCGCAACAUCCGCGCCCGCAGGUAUCUUCCUCCCCUGCCCCUCACACCCACCAAAUGUUAUUACCCAUCCCAGAUCAUAGAUCUAAUACCACAAAACCCAUAUAUCCCA
.((((...(((.(((.......))))))(((((...........))))).............................))))(((((...)))))......................... ( -25.40)
>DroSim_CAF1 38025 120 - 1
UGGGAAAAGGGUCGCAACAUCCGCGCCCGCAGGUAUCUUCCUCCCCUGCCCCUCACACCCACCAAAUGUUAUUACCCAUCCCAGAUCAUAGAUCUAAUACCACAAAACCCAUAUAUCCCA
.((((...(((.(((.......))))))(((((...........))))).............................))))(((((...)))))......................... ( -25.40)
>DroEre_CAF1 37640 113 - 1
UGGGAAAAGGGUCGCAACAUCCGCGCCCGCAGGUAUCUCC-----CUGUUCCUCACACCCACUAUAUGAUAUUACCCAUCCCAGAUCAUAGAUCUAAUACCACAAAACCCAU--AUCCCA
.((((...(((.(((.......))))))(((((......)-----)))).............................))))(((((...))))).................--...... ( -24.50)
>DroYak_CAF1 36740 113 - 1
UGGGAAAAGGGUCGCAACAUCCGCGCCCGCAGGUAUCUCC-----CUUUUUCUCCCACCCACAAAAUGAUAUUACCCAUCCCAGAUCAUAGAUCUAAUACCACAAAACCCAU--AUCCCA
.((((...(((.(((.......))))))...(((((....-----....................(((........)))...(((((...))))).)))))...........--.)))). ( -23.10)
>consensus
UGGGAAAAGGGUCGCAACAUCCGCGCCCGCAGGUAUCUCCCUCCCCUGCCCCUCACACCCACCAAAUGAUAUUACCCAUCCCAGAUCAUAGAUCUAAUACCACAAAACCCAU__AUCCCA
.((((...(((.(((.......))))))...(((((.............................(((........)))...(((((...))))).)))))..............)))). (-22.88 = -22.88 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	4,434,290 – 4,434,410
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.05
Mean single sequence MFE	-36.24
Consensus MFE	-32.88
Energy contribution	-32.96
Covariance contribution	0.08
Combinations/Pair	1.14
Mean z-score	-2.39
Structure conservation index	0.91
SVM decision value	3.73
SVM RNA-class probability	0.999570
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4434290 120 - 22224390
AGGUGAUGAAAUCAUGCGGGCUCCCCGCGUUUUUAGCCAAUGGGAAAAGGGUCGCAACAUCCGCGCCCGCAGGUAUCUACCUCCCCAGCCCCUCACACCCACCAAAUGAUAUUACCCAUC
.((((.(((....(((((((...))))))).....((...((((....(((.(((.......))))))..((((....)))).))))))...)))))))..................... ( -34.80)
>DroSec_CAF1 36696 120 - 1
AGGUGAUGAAAUCAUGCGGGCUCCCCGCGUUUUUAGCCAAUGGGAAAAGGGUCGCAACAUCCGCGCCCGCAGGUAUCUUCCUCCCCUGCCCCUCACACCCACCAAAUGUUAUUACCCAUC
.((((((((....(((((((...)))))))..........((((....(((.(((.......))))))(((((...........)))))........)))).......)))))))).... ( -39.40)
>DroSim_CAF1 38065 120 - 1
AGGUGAUGAAAUCAUGCGGGCUCCCCGCGUUUUUAGCCAAUGGGAAAAGGGUCGCAACAUCCGCGCCCGCAGGUAUCUUCCUCCCCUGCCCCUCACACCCACCAAAUGUUAUUACCCAUC
.((((((((....(((((((...)))))))..........((((....(((.(((.......))))))(((((...........)))))........)))).......)))))))).... ( -39.40)
>DroEre_CAF1 37678 115 - 1
AGGUGAUGAAAUCAUGCGGGCUCCCCGUGUUUUUAGCCAAUGGGAAAAGGGUCGCAACAUCCGCGCCCGCAGGUAUCUCC-----CUGUUCCUCACACCCACUAUAUGAUAUUACCCAUC
.((((((...((((((((((...)))))............((((....(((.(((.......))))))(((((......)-----))))........))))....))))))))))).... ( -35.40)
>DroYak_CAF1 36778 115 - 1
AGGUGAUGAAAUCAUGCGGGCUCCCUGCAUUUUUAGCCAAUGGGAAAAGGGUCGCAACAUCCGCGCCCGCAGGUAUCUCC-----CUUUUUCUCCCACCCACAAAAUGAUAUUACCCAUC
.((((((...(((((((((((((((.((.......))....))))...((((......))))..))))))(((......)-----))..................))))))))))).... ( -32.20)
>consensus
AGGUGAUGAAAUCAUGCGGGCUCCCCGCGUUUUUAGCCAAUGGGAAAAGGGUCGCAACAUCCGCGCCCGCAGGUAUCUCCCUCCCCUGCCCCUCACACCCACCAAAUGAUAUUACCCAUC
.(((((((.....(((((((...)))))))..........((((....(((.(((.......))))))(((((...........)))))........))))........))))))).... (-32.88 = -32.96 +   0.08)

alignment

secondary structure

dotplot

Window 1

Location	4,434,410 – 4,434,530
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.64
Mean single sequence MFE	-36.14
Consensus MFE	-32.14
Energy contribution	-32.34
Covariance contribution	0.20
Combinations/Pair	1.12
Mean z-score	-2.75
Structure conservation index	0.89
SVM decision value	4.06
SVM RNA-class probability	0.999780
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4434410 120 + 22224390
UAUGUAAUCAUCAAAUGAAGAGGGGACCUCGAAUUGGAUGCAAAGUGGAGGCCUCCACGGCAGACAAAUCAAUAAAAUGUCUGUAUCUGUAUCUGGUUGGUUCUCCCAGUUCUUUUUUUU
............(((.(((((.((((...(.(((..((((((..(((((....))))).(((((((...........)))))))...))))))..))).)...))))...))))).))). ( -38.30)
>DroSec_CAF1 36816 119 + 1
UAUGUAAUCAUCAAAUGAAGAGGGAACCUCGAAUUGGAUGCAAAGUGGAGGCCCUCACGGCAGACAAAUCAAUAAAAUGUCUGUAUCUGUAUCUGGUUGGUUCUCCCAGUUCUUU-UUCU
................((((((((((((...(((..((((((..((((......)))).(((((((...........)))))))...))))))..)))))))))).....)))))-.... ( -31.90)
>DroSim_CAF1 38185 120 + 1
UAUGUAAUCAUCAAAUGAAGAGGGGACUGCGAAUUGGAUUGAAAGUGGAGGCCUCCACGGCAGACAAAUCAAUAAAAUGUCUGUAUCAGUAUCUGGUUGGUUCUCCCAGUUCUUUUUUCU
................(((((((((((((..(((..((((((..(((((....))))).(((((((...........))))))).)))..)))..)))((....))))))))))))))). ( -36.70)
>DroEre_CAF1 37793 115 + 1
UAUGUAAUCAUCAAAUGAAGAGGGAACCUCGAAUUGGAUGCAAAGUGGAGGCCUUCACGGCAGACAAAUCAAUAAAAUGUCUGUAUCUGUAUCUGGUUGGUUCUCCUUGUGUUUU-----
...................(((((((((...(((..((((((..(((((....))))).(((((((...........)))))))...))))))..)))))))).)))).......----- ( -34.80)
>DroYak_CAF1 36893 117 + 1
UAUGUAAUCAUCAACUGAAGAGGGGACCUCGAAUUGGAUGCAAAGUGGAGGCCUCCACGACAGACAAAUCAAUAAAAUGUCUGUAUCUGUAUCUGGUCGGUUCUCUCAGUUUUUUUU---
...................(((((((((....((..((((((..(((((....))))).(((((((...........)))))))...))))))..)).)))))))))..........--- ( -39.00)
>consensus
UAUGUAAUCAUCAAAUGAAGAGGGGACCUCGAAUUGGAUGCAAAGUGGAGGCCUCCACGGCAGACAAAUCAAUAAAAUGUCUGUAUCUGUAUCUGGUUGGUUCUCCCAGUUCUUUUUU_U
.......((.((....)).))(((((((...(((..((((((..(((((....))))).(((((((...........)))))))...))))))..))))))))))............... (-32.14 = -32.34 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:57 2006