Locus 2346

Sequence ID 2R_DroMel_CAF1
Location 8,555,553 – 8,555,710
Length 157
Max. P 0.999232
window3869 window3870 window3871

overview

Window 9

Location 8,555,553 – 8,555,670
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.56
Mean single sequence MFE -31.18
Consensus MFE -21.85
Energy contribution -21.97
Covariance contribution 0.12
Combinations/Pair 1.14
Mean z-score -1.57
Structure conservation index 0.70
SVM decision value -0.05
SVM RNA-class probability 0.507665
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8555553 117 - 20766785
A--AGAUAUCGUGCUGUGAAUGAAAUUGCCAUCUAAAGUGGCUUUUGCUAUCGAUUUCGAUAGCUGGCAUCAAUUGCCGCUCGAUGAAACCGAAAUGCGAC-CCGUCGACCGCAGAAAAU
.--...(((((.((.........((..(((((.....)))))..))(((((((....))))))).((((.....)))))).))))).........((((..-........))))...... ( -33.70)
>DroSec_CAF1 31182 118 - 1
A-AAGAUAUCGUGCUGUGAAUGAAAUUCCCAUCUAAAGUGGUUUUUGCUAUCGAUUUCGAUAGCUGGCAUCAAUAGCCGCUCGAUGAAACCGAAAUGCGAC-CCGUCGACCGCAGAAAAU
.-...........(((((..(((...((.(((......(((((((.(((((((....))))))).(((.......))).......)))))))..))).)).-...)))..)))))..... ( -28.50)
>DroSim_CAF1 34755 118 - 1
A-AAGAUAUCGUGCUCUGAAUGAAAUUCCCAUCUAAAGUGGUUUUUGCUAUCGAUUUCGAUAGCUGGCAUCAAUUGCCGCUCGAUGAAACUGAAAUGCGAC-CCGUCGACCGCAGAAAAU
.-....(((((.((..............((((.....)))).....(((((((....))))))).((((.....)))))).)))))...(((.....(((.-...)))....)))..... ( -32.20)
>DroEre_CAF1 20079 119 - 1
UAAUGAUAUAGUGCCAUGAAUGAAAUA-CCAUAUAUGGCGUCAUUGGCUAUCGAUUUCGAUAGCUGGCAUCGAUUGCCGCUCGAUGAAACCGAAAUGCGACCCCGUCGACCGCAGAAAAU
.((((((.....((((((.(((.....-.))).))))))))))))((((((((....))))))))((((.....))))((((((((....((.....))....))))))..))....... ( -37.90)
>DroYak_CAF1 34429 101 - 1
----------AUACAAUGAAUGAAAUU-CCAUAUAUAGUGAAACUGGCUAUCGAUUUCGAUUGCUGACGUCGAUUGCCGCUCGAUGAAACCGAA--------CCGUCGACCGCAGAAAAU
----------.(((.(((.(((.....-.))).))).))).....(((.((((((.(((.....))).)))))).)))((((((((........--------.))))))..))....... ( -23.60)
>consensus
A_AAGAUAUCGUGCUAUGAAUGAAAUU_CCAUCUAAAGUGGCUUUUGCUAUCGAUUUCGAUAGCUGGCAUCAAUUGCCGCUCGAUGAAACCGAAAUGCGAC_CCGUCGACCGCAGAAAAU
...........((((.((.(((.......))).)).))))......(((((((....))))))).((((.....))))((((((((.................))))))..))....... (-21.85 = -21.97 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 8,555,592 – 8,555,710
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 72.98
Mean single sequence MFE -23.43
Consensus MFE -16.28
Energy contribution -16.52
Covariance contribution 0.24
Combinations/Pair 1.17
Mean z-score -2.31
Structure conservation index 0.69
SVM decision value 2.79
SVM RNA-class probability 0.997022
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8555592 118 + 20766785
GCGGCAAUUGAUGCCAGCUAUCGAAAUCGAUAGCAAAAGCCACUUUAGAUGGCAAUUUCAUUCACAGCACGAUAUCU--UUACAACUGAAAGUUAAAAUAAAGCGGUAAAUAAAUACAAA
((((((.....)))).(((((((....)))))))....(((((....).)))).............))........(--((((..((..............))..))))).......... ( -26.64)
>DroSec_CAF1 31221 119 + 1
GCGGCUAUUGAUGCCAGCUAUCGAAAUCGAUAGCAAAAACCACUUUAGAUGGGAAUUUCAUUCACAGCACGAUAUCUU-UUACAACUGAAACUUAAAAUAAAGCGCUAAAUAAAUAAGAA
(((((.......))).(((((((....))))))).........(((((.((..((......((.......)).....)-)..)).)))))............))................ ( -21.30)
>DroSim_CAF1 34794 114 + 1
GCGGCAAUUGAUGCCAGCUAUCGAAAUCGAUAGCAAAAACCACUUUAGAUGGGAAUUUCAUUCAGAGCACGAUAUCUU-UUACAACUAAAUGUUA---UUCAGCG--GAAUAAAUAAAAA
((((((.....)))).(((((((....))))))).....((((....).)))((((..((((.((.............-......)).))))..)---))).)).--............. ( -24.11)
>DroEre_CAF1 20119 108 + 1
GCGGCAAUCGAUGCCAGCUAUCGAAAUCGAUAGCCAAUGACGCCAUAUAUGG-UAUUUCAUUCAUGGCACUAUAUCAUUAUAUAACUAAAUGCUUAGAUAAAA----------AGAAU-A
((((((.....)))).(((((((....))))))).......(((((..((((-....))))..))))).......................))..........----------.....-. ( -27.20)
>DroYak_CAF1 34461 95 + 1
GCGGCAAUCGACGUCAGCAAUCGAAAUCGAUAGCCAGUUUCACUAUAUAUGG-AAUUUCAUUCAUUGUAU-------------AACAAAAUGCUAAAAUAAAA----------AUAAU-A
(((((.(((((..((.......))..))))).)))........(((((((((-(......)))).)))))-------------).......))..........----------.....-. ( -17.90)
>consensus
GCGGCAAUUGAUGCCAGCUAUCGAAAUCGAUAGCAAAAACCACUUUAGAUGG_AAUUUCAUUCACAGCACGAUAUCUU_UUACAACUAAAUGUUAAAAUAAAGCG___AAUAAAUAAAAA
..(((.......))).(((((((....)))))))........((((..((((.....))))..))))..................................................... (-16.28 = -16.52 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 8,555,592 – 8,555,710
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.98
Mean single sequence MFE -28.71
Consensus MFE -15.32
Energy contribution -15.44
Covariance contribution 0.12
Combinations/Pair 1.20
Mean z-score -2.78
Structure conservation index 0.53
SVM decision value 3.45
SVM RNA-class probability 0.999232
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8555592 118 - 20766785
UUUGUAUUUAUUUACCGCUUUAUUUUAACUUUCAGUUGUAA--AGAUAUCGUGCUGUGAAUGAAAUUGCCAUCUAAAGUGGCUUUUGCUAUCGAUUUCGAUAGCUGGCAUCAAUUGCCGC
......(((((((((.((..((((((.((........)).)--)))))....)).)))))))))...(((((.....)))))....(((((((....))))))).((((.....)))).. ( -35.50)
>DroSec_CAF1 31221 119 - 1
UUCUUAUUUAUUUAGCGCUUUAUUUUAAGUUUCAGUUGUAA-AAGAUAUCGUGCUGUGAAUGAAAUUCCCAUCUAAAGUGGUUUUUGCUAUCGAUUUCGAUAGCUGGCAUCAAUAGCCGC
...((((((((..(((((..((((((...............-))))))..))))))))))))).....((((.....)))).....(((((((....))))))).(((.......))).. ( -28.46)
>DroSim_CAF1 34794 114 - 1
UUUUUAUUUAUUC--CGCUGAA---UAACAUUUAGUUGUAA-AAGAUAUCGUGCUCUGAAUGAAAUUCCCAUCUAAAGUGGUUUUUGCUAUCGAUUUCGAUAGCUGGCAUCAAUUGCCGC
............(--(((((((---(..(((((((..(((.-..(....).))).)))))))..))))........))))).....(((((((....))))))).((((.....)))).. ( -29.60)
>DroEre_CAF1 20119 108 - 1
U-AUUCU----------UUUUAUCUAAGCAUUUAGUUAUAUAAUGAUAUAGUGCCAUGAAUGAAAUA-CCAUAUAUGGCGUCAUUGGCUAUCGAUUUCGAUAGCUGGCAUCGAUUGCCGC
.-.....----------..........((............((((((.....((((((.(((.....-.))).))))))))))))((((((((....))))))))((((.....)))))) ( -30.60)
>DroYak_CAF1 34461 95 - 1
U-AUUAU----------UUUUAUUUUAGCAUUUUGUU-------------AUACAAUGAAUGAAAUU-CCAUAUAUAGUGAAACUGGCUAUCGAUUUCGAUUGCUGACGUCGAUUGCCGC
.-.....----------..........((.....(((-------------.(((.(((.(((.....-.))).))).))).))).(((.((((((.(((.....))).)))))).))))) ( -19.40)
>consensus
UUAUUAUUUAUU___CGCUUUAUUUUAACAUUUAGUUGUAA_AAGAUAUCGUGCUAUGAAUGAAAUU_CCAUCUAAAGUGGCUUUUGCUAUCGAUUUCGAUAGCUGGCAUCAAUUGCCGC
...................................................((((.((.(((.......))).)).))))......(((((((....))))))).((((.....)))).. (-15.32 = -15.44 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:33 2006