Locus 5892

Sequence ID 2R_DroMel_CAF1
Location 18,606,404 – 18,606,631
Length 227
Max. P 0.948013
window9458 window9459 window9460 window9461 window9462

overview

Window 8

Location 18,606,404 – 18,606,511
Length 107
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 94.73
Mean single sequence MFE -30.86
Consensus MFE -28.92
Energy contribution -28.68
Covariance contribution -0.24
Combinations/Pair 1.04
Mean z-score -1.43
Structure conservation index 0.94
SVM decision value 1.38
SVM RNA-class probability 0.948013
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18606404 107 + 20766785
C---UGCUCAUCCGCUGCACUGCUCAUCCGGAGACAAUCGUGAGCGAAAUUUAAAUGCUGCUGACUUUGCAGCUCACUGAAUGACAACUAUACGGCGAGGGGAACAAAAA
.---((.((..((((((....((((((..(....)....))))))(..(((((...(((((.......)))))....)))))..).......))))).)..)).)).... ( -28.30)
>DroSec_CAF1 16005 107 + 1
C---UACUCAUCCGCUGCACUGCUCAUCCGGAGACAAUCGUGAGCGAAAUUUAAAUGCUGCUGACUGAGCAGCUCUCUGAAUGACAACUAUACGGCGAGGGGAACAAAAA
.---..(((...(((((...((.((((.((((((...(((....))).........((((((.....)))))))))))).))))))......)))))..)))........ ( -31.00)
>DroSim_CAF1 16635 107 + 1
C---UGCUCAUCCGCUGCACUGCUCAUCCGGAGACAAUCGUGAGCGAAAUUUAAAUGCUGCUGACUUUGCAGCUCACUGAAUGACAACUAUACGGCGAGGGGAACAAAAA
.---((.((..((((((....((((((..(....)....))))))(..(((((...(((((.......)))))....)))))..).......))))).)..)).)).... ( -28.30)
>DroEre_CAF1 16009 106 + 1
----UGCUCAUCCGCUGCACUGCUCAUCCGGAGACAAUCGUGAGCGAAAUUUAAAUGCUGCUGACUUUGCAGCUCACUGAAUGACAACUAUACAGCGAGGGGAAGAAAAA
----...((.(((.((((...((((((..(....)....))))))(..(((((...(((((.......)))))....)))))..).........)).)).))).)).... ( -29.00)
>DroYak_CAF1 15945 110 + 1
CUGCUCCUCAUCCGCUGCACUGCUCAUCCGGAGACAAUCGUGAGCGAAAUUUAAAUGCUGCUGACUUUGCAGCUCACUGAAUGGCAAGUGUACAGCGAGGGGAACAAAAA
.((.(((((...(((((((((((((((..(....)....))))))(..(((((...(((((.......)))))....)))))..).))))..))))).))))).)).... ( -37.70)
>consensus
C___UGCUCAUCCGCUGCACUGCUCAUCCGGAGACAAUCGUGAGCGAAAUUUAAAUGCUGCUGACUUUGCAGCUCACUGAAUGACAACUAUACGGCGAGGGGAACAAAAA
......(((...(((((....((((((..(....)....))))))(..(((((...(((((.......)))))....)))))..).......)))))..)))........ (-28.92 = -28.68 +  -0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 18,606,431 – 18,606,551
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.00
Mean single sequence MFE -27.71
Consensus MFE -22.74
Energy contribution -23.74
Covariance contribution 1.00
Combinations/Pair 1.06
Mean z-score -1.57
Structure conservation index 0.82
SVM decision value 0.22
SVM RNA-class probability 0.641519
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18606431 120 + 20766785
GAGACAAUCGUGAGCGAAAUUUAAAUGCUGCUGACUUUGCAGCUCACUGAAUGACAACUAUACGGCGAGGGGAACAAAAAUAAUGGAAAGGCAACAAGCGCAGCAAAAAAUGUCGAUUGA
..((((.(((....)))........((((((...((((.((.(((.(((.(((.....))).))).)))(....)........)).))))((.....)))))))).....))))...... ( -28.80)
>DroSec_CAF1 16032 120 + 1
GAGACAAUCGUGAGCGAAAUUUAAAUGCUGCUGACUGAGCAGCUCUCUGAAUGACAACUAUACGGCGAGGGGAACAAAAAUAAUGGAAAGGCAACAAGCGCAGCAAAAAAUGUCGAUUGA
....(((((.........(((((...((((((.....))))))....)))))((((........(((..(....)..............(....)...))).........))))))))). ( -24.73)
>DroSim_CAF1 16662 120 + 1
GAGACAAUCGUGAGCGAAAUUUAAAUGCUGCUGACUUUGCAGCUCACUGAAUGACAACUAUACGGCGAGGGGAACAAAAAUAAUGGAAAGGCAACAAGCGCAGCAAAAAAUGUCGAUUGA
..((((.(((....)))........((((((...((((.((.(((.(((.(((.....))).))).)))(....)........)).))))((.....)))))))).....))))...... ( -28.80)
>DroEre_CAF1 16035 120 + 1
GAGACAAUCGUGAGCGAAAUUUAAAUGCUGCUGACUUUGCAGCUCACUGAAUGACAACUAUACAGCGAGGGGAAGAAAAAUAAUGGAAAAGCAACAAGCGCAGCAAAAAAUCCCGAUUGA
....((((((.((............((((((...((((.(..(((.(((.(((.....))).))).)))).))))...............((.....)))))))).....)).)))))). ( -26.33)
>DroYak_CAF1 15975 120 + 1
GAGACAAUCGUGAGCGAAAUUUAAAUGCUGCUGACUUUGCAGCUCACUGAAUGGCAAGUGUACAGCGAGGGGAACAAAAAUAAUGGAAAAGCAACAAGCGCAGCAAAAAAUGUCGAUUGA
..((((.(((....)))........((((((...((((((.(..((((........))))..).))))))....................((.....)))))))).....))))...... ( -29.90)
>consensus
GAGACAAUCGUGAGCGAAAUUUAAAUGCUGCUGACUUUGCAGCUCACUGAAUGACAACUAUACGGCGAGGGGAACAAAAAUAAUGGAAAGGCAACAAGCGCAGCAAAAAAUGUCGAUUGA
..((((.(((....)))........((((((...((((.((.(((.(((.(((.....))).))).)))(....)........)).))))((.....)))))))).....))))...... (-22.74 = -23.74 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 18,606,471 – 18,606,591
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.33
Mean single sequence MFE -25.45
Consensus MFE -20.34
Energy contribution -20.82
Covariance contribution 0.48
Combinations/Pair 1.11
Mean z-score -1.54
Structure conservation index 0.80
SVM decision value 0.14
SVM RNA-class probability 0.602041
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18606471 120 - 20766785
AUUCGCUUGAGCGAAAUACCAUUUUGUUGAUUGAACAUUUUCAAUCGACAUUUUUUGCUGCGCUUGUUGCCUUUCCAUUAUUUUUGUUCCCCUCGCCGUAUAGUUGUCAUUCAGUGAGCU
....((...(((((((........(((((((((((....)))))))))))..)))))))))(((..(((.....(.(((((....((.......))...))))).).....)))..))). ( -25.30)
>DroSec_CAF1 16072 120 - 1
AUUCGAUCGAGCGAAAUGCCAUUUUGUUGAUUGAACAUUUUCAAUCGACAUUUUUUGCUGCGCUUGUUGCCUUUCCAUUAUUUUUGUUCCCCUCGCCGUAUAGUUGUCAUUCAGAGAGCU
...(((.((((((....((.....(((((((((((....)))))))))))......))..)))))))))................................((((.((.....)).)))) ( -26.30)
>DroSim_CAF1 16702 120 - 1
AUUCGCUCGAGCGAAAUGCCAUUUUGUUGAUUGAACAUUUUCAAUCGACAUUUUUUGCUGCGCUUGUUGCCUUUCCAUUAUUUUUGUUCCCCUCGCCGUAUAGUUGUCAUUCAGUGAGCU
....((.((((((....((.....(((((((((((....)))))))))))......))..))))))..)).....................(((((.(.............).))))).. ( -27.82)
>DroEre_CAF1 16075 120 - 1
AUUUGUUUGAGCGAAAUGCCAUUUUGUUGAUUGAACAUUUUCAAUCGGGAUUUUUUGCUGCGCUUGUUGCUUUUCCAUUAUUUUUCUUCCCCUCGCUGUAUAGUUGUCAUUCAGUGAGCU
....((.((((((....((.....(.(((((((((....))))))))).)......))..))))))..)).....................(((((((.............))))))).. ( -23.72)
>DroYak_CAF1 16015 120 - 1
AUUUGUUUGAGCGAAAUGCCAUUUUGCUGAUUGAACAUUUUCAAUCGACAUUUUUUGCUGCGCUUGUUGCUUUUCCAUUAUUUUUGUUCCCCUCGCUGUACACUUGCCAUUCAGUGAGCU
........((((((((.((.....((.((((((((....)))))))).))......))...((.....))...........))))))))..(((((((.............))))))).. ( -24.12)
>consensus
AUUCGCUUGAGCGAAAUGCCAUUUUGUUGAUUGAACAUUUUCAAUCGACAUUUUUUGCUGCGCUUGUUGCCUUUCCAUUAUUUUUGUUCCCCUCGCCGUAUAGUUGUCAUUCAGUGAGCU
....((.((((((....((.....(((((((((((....)))))))))))......))..))))))..)).....................(((((.(.............).))))).. (-20.34 = -20.82 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 18,606,511 – 18,606,631
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.50
Mean single sequence MFE -30.91
Consensus MFE -22.06
Energy contribution -22.58
Covariance contribution 0.52
Combinations/Pair 1.14
Mean z-score -2.35
Structure conservation index 0.71
SVM decision value 0.64
SVM RNA-class probability 0.807843
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18606511 120 + 20766785
UAAUGGAAAGGCAACAAGCGCAGCAAAAAAUGUCGAUUGAAAAUGUUCAAUCAACAAAAUGGUAUUUCGCUCAAGCGAAUUGUUAAAGGCGCUUCCUGAAAUGUGGCGCAAGCUCAAUAU
....((((.(....)..((((.........(((.(((((((....))))))).)))...(..((.(((((....))))).))..)...)))))))).....((.(((....))))).... ( -33.10)
>DroSec_CAF1 16112 114 + 1
UAAUGGAAAGGCAACAAGCGCAGCAAAAAAUGUCGAUUGAAAAUGUUCAAUCAACAAAAUGGCAUUUCGCUCGAUCGAAUUGUUGAAGGCGAUUCCUGGAAUGUGGCGCA------AUAU
.........(....)..((((.........(((.(((((((....))))))).))).....((((((((...(((((..((....))..)))))..)))))))).)))).------.... ( -29.10)
>DroSim_CAF1 16742 120 + 1
UAAUGGAAAGGCAACAAGCGCAGCAAAAAAUGUCGAUUGAAAAUGUUCAAUCAACAAAAUGGCAUUUCGCUCGAGCGAAUUGUUGAAGGCGAUUCCGGGAAUGUGGCGCAAGCUCAAUAU
...(((((.(....)...(((.........(((.(((((((....))))))).)))....((((.(((((....))))).))))....))).)))))....((.(((....))))).... ( -33.30)
>DroEre_CAF1 16115 120 + 1
UAAUGGAAAAGCAACAAGCGCAGCAAAAAAUCCCGAUUGAAAAUGUUCAAUCAACAAAAUGGCAUUUCGCUCAAACAAAUUGUUGAAGGCGAUUCGUGAAAUGUGGCGCAGGCUUGAUAG
........((((.....((((.............(((((((....))))))).........(((((((((...(((.....)))(((.....)))))))))))).))))..))))..... ( -28.70)
>DroYak_CAF1 16055 120 + 1
UAAUGGAAAAGCAACAAGCGCAGCAAAAAAUGUCGAUUGAAAAUGUUCAAUCAGCAAAAUGGCAUUUCGCUCAAACAAAUUGUCGAAGGCGAUUCUUAAAAUGUGGUGCCAGCGCGAUAG
.................((((.........(((.(((((((....))))))).)))...((((((..(((.......((((((.....))))))........)))))))))))))..... ( -30.36)
>consensus
UAAUGGAAAGGCAACAAGCGCAGCAAAAAAUGUCGAUUGAAAAUGUUCAAUCAACAAAAUGGCAUUUCGCUCAAACGAAUUGUUGAAGGCGAUUCCUGAAAUGUGGCGCAAGCUCAAUAU
.................((((.........(((.(((((((....))))))).))).....((((((((......)(((((((.....)))))))..))))))).))))........... (-22.06 = -22.58 +   0.52)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 18,606,511 – 18,606,631
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.50
Mean single sequence MFE -27.10
Consensus MFE -21.46
Energy contribution -21.78
Covariance contribution 0.32
Combinations/Pair 1.12
Mean z-score -1.77
Structure conservation index 0.79
SVM decision value 0.70
SVM RNA-class probability 0.825501
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18606511 120 - 20766785
AUAUUGAGCUUGCGCCACAUUUCAGGAAGCGCCUUUAACAAUUCGCUUGAGCGAAAUACCAUUUUGUUGAUUGAACAUUUUCAAUCGACAUUUUUUGCUGCGCUUGUUGCCUUUCCAUUA
....((.((....)))).....(((.((((((.........(((((....))))).........(((((((((((....))))))))))).........)))))).)))........... ( -30.50)
>DroSec_CAF1 16112 114 - 1
AUAU------UGCGCCACAUUCCAGGAAUCGCCUUCAACAAUUCGAUCGAGCGAAAUGCCAUUUUGUUGAUUGAACAUUUUCAAUCGACAUUUUUUGCUGCGCUUGUUGCCUUUCCAUUA
....------..............((((..((..((........)).((((((....((.....(((((((((((....)))))))))))......))..))))))..))..)))).... ( -27.40)
>DroSim_CAF1 16742 120 - 1
AUAUUGAGCUUGCGCCACAUUCCCGGAAUCGCCUUCAACAAUUCGCUCGAGCGAAAUGCCAUUUUGUUGAUUGAACAUUUUCAAUCGACAUUUUUUGCUGCGCUUGUUGCCUUUCCAUUA
...(((((...(((((........))...))).)))))......((.((((((....((.....(((((((((((....)))))))))))......))..))))))..)).......... ( -29.10)
>DroEre_CAF1 16115 120 - 1
CUAUCAAGCCUGCGCCACAUUUCACGAAUCGCCUUCAACAAUUUGUUUGAGCGAAAUGCCAUUUUGUUGAUUGAACAUUUUCAAUCGGGAUUUUUUGCUGCGCUUGUUGCUUUUCCAUUA
....((((((.(((....((..(.....((((.((.(((.....))).))))))..............(((((((....))))))))..))....))).).))))).............. ( -23.50)
>DroYak_CAF1 16055 120 - 1
CUAUCGCGCUGGCACCACAUUUUAAGAAUCGCCUUCGACAAUUUGUUUGAGCGAAAUGCCAUUUUGCUGAUUGAACAUUUUCAAUCGACAUUUUUUGCUGCGCUUGUUGCUUUUCCAUUA
.....((((.((((..............((((.((.(((.....))).))))))..........((.((((((((....)))))))).)).....))))))))................. ( -25.00)
>consensus
AUAUCGAGCUUGCGCCACAUUUCAGGAAUCGCCUUCAACAAUUCGCUUGAGCGAAAUGCCAUUUUGUUGAUUGAACAUUUUCAAUCGACAUUUUUUGCUGCGCUUGUUGCCUUUCCAUUA
........................((((..((....(((((..(((...(((((((........(((((((((((....)))))))))))..)))))))))).)))))))..)))).... (-21.46 = -21.78 +   0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:29 2006