Locus 10250

Sequence ID	3R_DroMel_CAF1
Location	27,458,911 – 27,459,050
Length	139
Max. P	0.996109

overview

Window 5

Location	27,458,911 – 27,459,018
Length	107
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	74.24
Mean single sequence MFE	-32.25
Consensus MFE	-16.58
Energy contribution	-17.45
Covariance contribution	0.87
Combinations/Pair	1.20
Mean z-score	-1.60
Structure conservation index	0.51
SVM decision value	-0.00
SVM RNA-class probability	0.532749
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27458911 107 + 27905053
AUUAUAUACCAGUCCUCACUGCUGCCAGACAUCCGUC--CAAUAGAGCUCGGCUCAGC-GGGCUCAACGGAGUACAGUAAGUACUCCUGACAGCCUCAAAGAGC----UA-AGAC
..........((..((....((((.(((((....)))--.....(((((((......)-))))))...(((((((.....))))))))).)))).....))..)----).-.... ( -32.00)
>DroSec_CAF1 14792 100 + 1
ACUAUAUACCAGUCCUCACUGCUGCCAGACGUCCGUC--CAAUAGAGCUCGGCUCAGC-GGGCUCAACGGAGUACAGUAAGUACUCCUGACAGCCCUCUU------------UCG
....................((((.(((((....)))--.....(((((((......)-))))))...(((((((.....))))))))).))))......------------... ( -30.20)
>DroSim_CAF1 14681 100 + 1
AUUAUAUACCAGUCCUCACUGCUGCCAGACGUCCGUC--CAAUAGAGCUCGGCUCAGC-GGGCUCAACGGAGUACAGUAAGUACUCUUGACAGCCUCGAU------------UCC
....................((((.(((((....)))--.....(((((((......)-))))))...(((((((.....))))))))).))))......------------... ( -27.50)
>DroEre_CAF1 14749 107 + 1
AUUAUGUGCCAGUCCUCACUGCUGUCAGCCAUCCGUC--CAACAGAGGCGGGCUCAGC-GGGCUCAGCGGAGUACAGUAAGUACUCCUGACAGCCUCAAAGAGC----UA-AGGA
........((((..((....((((((((((.((.(..--...).)))))(((((....-.)))))...(((((((.....)))))))))))))).....))..)----).-.)). ( -36.90)
>DroYak_CAF1 14881 107 + 1
AUUAUAGCCCAGUCCUCACUGCUGCCAAACAUCCGUC--GAAUGGAGCCGGGCUCAGC-GGGCUCAACGGAGUACAGUAAGUACUCCUGACAGCCUCAAAGAGC----UG-AGGA
............((((((((((((((.....(((((.--..)))))....)))..)))-))((((...(((((((.....)))))))(((.....)))..))))----))-)))) ( -39.40)
>DroPer_CAF1 17346 108 + 1
GUUAUUUCCAUGUACUCACUUAUGCCAGACUUCCUUGCUCAGCGGAGUC--GCUCAGUUGGGAGCUCUGAAGUACAGUGGACACUCCAG-----CACAAAGACCACGCUCAAUAC
......((((((((((..(....).((((.(((((.(((.((((....)--))).))).))))).)))).)))))).))))......((-----(...........)))...... ( -27.50)
>consensus
AUUAUAUACCAGUCCUCACUGCUGCCAGACAUCCGUC__CAAUAGAGCCCGGCUCAGC_GGGCUCAACGGAGUACAGUAAGUACUCCUGACAGCCUCAAAGAGC____U__AGAC
.........((((....)))).......................((((...))))....(((((....(((((((.....)))))))....)))))................... (-16.58 = -17.45 +   0.87)

alignment

secondary structure

dotplot

Window 6

Location	27,458,911 – 27,459,018
Length	107
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	74.24
Mean single sequence MFE	-38.13
Consensus MFE	-22.20
Energy contribution	-22.07
Covariance contribution	-0.13
Combinations/Pair	1.30
Mean z-score	-1.71
Structure conservation index	0.58
SVM decision value	0.86
SVM RNA-class probability	0.868026
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27458911 107 - 27905053
GUCU-UA----GCUCUUUGAGGCUGUCAGGAGUACUUACUGUACUCCGUUGAGCCC-GCUGAGCCGAGCUCUAUUG--GACGGAUGUCUGGCAGCAGUGAGGACUGGUAUAUAAU
((((-(.----((((..((.((((....(((((((.....)))))))....)))))-)..))))...(((((.(..--(((....)))..).)).))).)))))........... ( -37.90)
>DroSec_CAF1 14792 100 - 1
CGA------------AAGAGGGCUGUCAGGAGUACUUACUGUACUCCGUUGAGCCC-GCUGAGCCGAGCUCUAUUG--GACGGACGUCUGGCAGCAGUGAGGACUGGUAUAUAGU
(..------------..).(((((....(((((((.....)))))))....)))))-((((..((..(((((.(..--(((....)))..).)).)))..))..))))....... ( -38.30)
>DroSim_CAF1 14681 100 - 1
GGA------------AUCGAGGCUGUCAAGAGUACUUACUGUACUCCGUUGAGCCC-GCUGAGCCGAGCUCUAUUG--GACGGACGUCUGGCAGCAGUGAGGACUGGUAUAUAAU
(..------------.(((..(((((((.((((((.....))))))((((..(.((-(..((((...))))...))--).).))))..)))))))..)))...)........... ( -31.20)
>DroEre_CAF1 14749 107 - 1
UCCU-UA----GCUCUUUGAGGCUGUCAGGAGUACUUACUGUACUCCGCUGAGCCC-GCUGAGCCCGCCUCUGUUG--GACGGAUGGCUGACAGCAGUGAGGACUGGCACAUAAU
...(-((----(.((((((..((((((((((((((.....)))))))(((.((...-.)).)))..(((((((...--..)))).))))))))))..))))))))))........ ( -44.50)
>DroYak_CAF1 14881 107 - 1
UCCU-CA----GCUCUUUGAGGCUGUCAGGAGUACUUACUGUACUCCGUUGAGCCC-GCUGAGCCCGGCUCCAUUC--GACGGAUGUUUGGCAGCAGUGAGGACUGGGCUAUAAU
..((-((----(.((((((..((((((((((((((.....)))))))((((((...-((((....))))....)))--))).......)))))))..)))))))))))....... ( -43.90)
>DroPer_CAF1 17346 108 - 1
GUAUUGAGCGUGGUCUUUGUG-----CUGGAGUGUCCACUGUACUUCAGAGCUCCCAACUGAGC--GACUCCGCUGAGCAAGGAAGUCUGGCAUAAGUGAGUACAUGGAAAUAAC
.........(((.((((((((-----(..((.(.(((.(((.....))).((((.......(((--(....))))))))..)))).))..))))))).)).)))........... ( -33.01)
>consensus
GCAU__A____GCUCUUUGAGGCUGUCAGGAGUACUUACUGUACUCCGUUGAGCCC_GCUGAGCCGAGCUCUAUUG__GACGGAUGUCUGGCAGCAGUGAGGACUGGUAUAUAAU
....................((((....(((((((.....)))))))....)))).......(((..(((((.........))).))..)))..((((....))))......... (-22.20 = -22.07 +  -0.13)

alignment

secondary structure

dotplot

Window 7

Location	27,458,949 – 27,459,050
Length	101
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	83.38
Mean single sequence MFE	-35.42
Consensus MFE	-24.56
Energy contribution	-24.80
Covariance contribution	0.24
Combinations/Pair	1.19
Mean z-score	-3.25
Structure conservation index	0.69
SVM decision value	2.39
SVM RNA-class probability	0.993312
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27458949 101 + 27905053
AAUAGAGCUCGGCUCAGCGGGCUCAACGGAGUACAGUAAGUACUCCUGACAGCCUCAAAGAGCUAAGAC-UUC-GAAGGAAUCAUUCAGUCGAACUGUUAAAC
(((((..((..((((...(((((....(((((((.....)))))))....)))))....))))..))..-(((-((..((.....))..)))))))))).... ( -34.40)
>DroSec_CAF1 14830 95 + 1
AAUAGAGCUCGGCUCAGCGGGCUCAACGGAGUACAGUAAGUACUCCUGACAGCCCUCUU-------UCGAGGC-UAAGGAAUCAUUCAGCCGAACUGUUAAAC
(((((...((((((.((.(((((....(((((((.....)))))))....))))).)).-------..((..(-....)..))....)))))).))))).... ( -32.70)
>DroSim_CAF1 14719 94 + 1
AAUAGAGCUCGGCUCAGCGGGCUCAACGGAGUACAGUAAGUACUCUUGACAGCCUCGAU-------UCC-UAC-GAAGGAAUCAUUCAGCCGAACUGUUAAAC
(((((...((((((....(((((....(((((((.....)))))))....))))).(((-------(((-(..-..)))))))....)))))).))))).... ( -35.50)
>DroEre_CAF1 14787 101 + 1
AACAGAGGCGGGCUCAGCGGGCUCAGCGGAGUACAGUAAGUACUCCUGACAGCCUCAAAGAGCUAAGGA-UUC-GGAGGAAUCAUUCAGCCGAGCAGUUAAAC
(((.((((((((((.....)))))...(((((((.....))))))).....)))))...(.(((...((-(((-....)))))....)))).....))).... ( -36.50)
>DroYak_CAF1 14919 102 + 1
AAUGGAGCCGGGCUCAGCGGGCUCAACGGAGUACAGUAAGUACUCCUGACAGCCUCAAAGAGCUGAGGA-UUCAGGGGGAAUCAUUCAGCCGAACUGUUAAAC
....(((((.(......).)))))...(((((((.....)))))))((((((..((...(.((((((((-(((.....))))).))))))))).))))))... ( -38.00)
>consensus
AAUAGAGCUCGGCUCAGCGGGCUCAACGGAGUACAGUAAGUACUCCUGACAGCCUCAAAGAGCU_AGCA_UUC_GAAGGAAUCAUUCAGCCGAACUGUUAAAC
(((((...((((((....(((((....(((((((.....)))))))....)))))......................(((....))))))))).))))).... (-24.56 = -24.80 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	27,458,949 – 27,459,050
Length	101
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	83.38
Mean single sequence MFE	-36.86
Consensus MFE	-26.21
Energy contribution	-25.61
Covariance contribution	-0.60
Combinations/Pair	1.21
Mean z-score	-3.40
Structure conservation index	0.71
SVM decision value	2.65
SVM RNA-class probability	0.996109
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27458949 101 - 27905053
GUUUAACAGUUCGACUGAAUGAUUCCUUC-GAA-GUCUUAGCUCUUUGAGGCUGUCAGGAGUACUUACUGUACUCCGUUGAGCCCGCUGAGCCGAGCUCUAUU
........(((((((....((((..((((-(((-(........))))))))..))))(((((((.....)))))))))))))).....((((...)))).... ( -35.70)
>DroSec_CAF1 14830 95 - 1
GUUUAACAGUUCGGCUGAAUGAUUCCUUA-GCCUCGA-------AAGAGGGCUGUCAGGAGUACUUACUGUACUCCGUUGAGCCCGCUGAGCCGAGCUCUAUU
.......(((((((((((.....))..((-((.((..-------..))(((((....(((((((.....)))))))....))))))))))))))))))..... ( -40.50)
>DroSim_CAF1 14719 94 - 1
GUUUAACAGUUCGGCUGAAUGAUUCCUUC-GUA-GGA-------AUCGAGGCUGUCAAGAGUACUUACUGUACUCCGUUGAGCCCGCUGAGCCGAGCUCUAUU
.......(((((((((.(..(((((((..-..)-)))-------)))(.((((.....((((((.....)))))).....)))))..).)))))))))..... ( -37.70)
>DroEre_CAF1 14787 101 - 1
GUUUAACUGCUCGGCUGAAUGAUUCCUCC-GAA-UCCUUAGCUCUUUGAGGCUGUCAGGAGUACUUACUGUACUCCGCUGAGCCCGCUGAGCCCGCCUCUGUU
............((((((..(((((....-)))-)).))))))....(((((.....(((((((.....)))))))(((.((....)).)))..))))).... ( -35.90)
>DroYak_CAF1 14919 102 - 1
GUUUAACAGUUCGGCUGAAUGAUUCCCCCUGAA-UCCUCAGCUCUUUGAGGCUGUCAGGAGUACUUACUGUACUCCGUUGAGCCCGCUGAGCCCGGCUCCAUU
......(((...((((((..(((((.....)))-)).))))))..))).((((....(((((((.....)))))))....)))).((((....))))...... ( -34.50)
>consensus
GUUUAACAGUUCGGCUGAAUGAUUCCUUC_GAA_GCCU_AGCUCUUUGAGGCUGUCAGGAGUACUUACUGUACUCCGUUGAGCCCGCUGAGCCGAGCUCUAUU
(((((.(.(((((((....((((.((((...................))))..))))(((((((.....))))))))))))))..).)))))........... (-26.21 = -25.61 +  -0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:52:39 2006