Locus 8712

Sequence ID 3R_DroMel_CAF1
Location 23,288,670 – 23,288,798
Length 128
Max. P 0.969519
window13989 window13990 window13991 window13992

overview

Window 9

Location 23,288,670 – 23,288,777
Length 107
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 72.41
Mean single sequence MFE -33.72
Consensus MFE -13.79
Energy contribution -14.76
Covariance contribution 0.97
Combinations/Pair 1.11
Mean z-score -1.82
Structure conservation index 0.41
SVM decision value 0.06
SVM RNA-class probability 0.562856
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23288670 107 + 27905053
GCUUCCUGGUG--AUGGUGAUGAUAAUGGUGCUGCUGC---UCCAAGUGCCGGUCAG-UGUGGCAACAAAUGUUGCCAAAGGCUGUGCCACAAUUCGUUUCAUUUGCGGCCAA
......(((((--((((.(((((...(((.((....))---.))).(((((((((..-..(((((((....)))))))..))))).).)))...))))))))))....)))). ( -35.10)
>DroSim_CAF1 89436 106 + 1
GCUUCCUGGUA--AUGGUGAUGAUGAUGCUGCUGCUGCUGCUCCAAGUGCCGGUCAG-UGUGGCAC--AAUGUUGCCAAAGGCUGUGC-AC-AUUCGUUUCAUUUGCGGCCAC
......((((.--..(((((.(((((.((.((....)).)).....(((((((((..-..(((((.--.....)))))..))))).))-))-..))))))))))....)))). ( -34.80)
>DroEre_CAF1 91759 103 + 1
GCUGCCCGGUG--AUGC-CAUCGUCAUGCUGC---UGC---UGCAAGUGCCGGUCAG-UGUGGCAACAAAUGUUGCCAAAUGCUGUGCCACAAUUCGUUUCAUUUGCGGCCCA
((.((.(((((--....-)))))....)).))---.((---((((((((..((((((-(.(((((((....)))))))...)))).)))((.....))..))))))))))... ( -39.10)
>DroWil_CAF1 94398 88 + 1
GUUUCCUGCUG--CA------------GUUGU---UGC---UACA---UCUGGUCAA-UGUGGCAACAAAUGUUGCCAG-UUCUGUGCCACAAUUCGUUUAAUUUGUGGCUAG
.....((((.(--((------------.((((---(((---((((---(.......)-))))))))))).))).).)))-..(((.(((((((..........)))))))))) ( -31.00)
>DroYak_CAF1 89048 93 + 1
GCAUCCUGGUG--AU------------GAUGA---UGC---UCCAAGUGCCGGUCAUCUGUGGCAACAAAUGUUGCCAAAUCCAGUGCCACAAUUCGUUUCAUUUGCGGCAAA
.....((((.(--((------------(((..---.((---.......))..))))))..(((((((....)))))))...))))((((.(((..........))).)))).. ( -29.60)
>DroAna_CAF1 82014 106 + 1
GUUUCCUGACCCGGCACGGCUGAUGAUGCUGA---UACUUUCCCAA---CUGGUCAG-UGUGGCAACAAAUGUUGCCAAAUGCCGAGCCACAAUUCGUUUAAUUUGCGGCCAC
...........(((((((((.......))))(---((((..((...---..))..))-)))((((((....))))))...))))).(((.(((..........))).)))... ( -32.70)
>consensus
GCUUCCUGGUG__AUG__GAUGAU_AUGCUGC___UGC___UCCAAGUGCCGGUCAG_UGUGGCAACAAAUGUUGCCAAAUGCUGUGCCACAAUUCGUUUCAUUUGCGGCCAA
.....(((((......................................))))).......(((((((....)))))))........(((.(((..........))).)))... (-13.79 = -14.76 +   0.97)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 23,288,670 – 23,288,777
Length 107
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 72.41
Mean single sequence MFE -30.10
Consensus MFE -17.69
Energy contribution -18.33
Covariance contribution 0.64
Combinations/Pair 1.18
Mean z-score -1.56
Structure conservation index 0.59
SVM decision value 0.73
SVM RNA-class probability 0.834509
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23288670 107 - 27905053
UUGGCCGCAAAUGAAACGAAUUGUGGCACAGCCUUUGGCAACAUUUGUUGCCACA-CUGACCGGCACUUGGA---GCAGCAGCACCAUUAUCAUCACCAU--CACCAGGAAGC
.(((((((((..........))))))).))(((..(((((((....)))))))..-......)))...(((.---((....)).))).........((..--.....)).... ( -27.20)
>DroSim_CAF1 89436 106 - 1
GUGGCCGCAAAUGAAACGAAU-GU-GCACAGCCUUUGGCAACAUU--GUGCCACA-CUGACCGGCACUUGGAGCAGCAGCAGCAGCAUCAUCAUCACCAU--UACCAGGAAGC
(((((((((.((.......))-.)-)).(((....(((((.....--.)))))..-)))...)))...((..((.((....)).))..))....)))...--........... ( -22.50)
>DroEre_CAF1 91759 103 - 1
UGGGCCGCAAAUGAAACGAAUUGUGGCACAGCAUUUGGCAACAUUUGUUGCCACA-CUGACCGGCACUUGCA---GCA---GCAGCAUGACGAUG-GCAU--CACCGGGCAGC
((((((((((..........))))))).(((((..((....))..))))))))..-(((.((((....(((.---(((---......)).)....-))).--..)))).))). ( -33.20)
>DroWil_CAF1 94398 88 - 1
CUAGCCACAAAUUAAACGAAUUGUGGCACAGAA-CUGGCAACAUUUGUUGCCACA-UUGACCAGA---UGUA---GCA---ACAAC------------UG--CAGCAGGAAAC
...(((((((.((....)).)))))))......-((.((..((.(((((((.(((-((.....))---))).---)))---)))).------------))--..)).)).... ( -27.90)
>DroYak_CAF1 89048 93 - 1
UUUGCCGCAAAUGAAACGAAUUGUGGCACUGGAUUUGGCAACAUUUGUUGCCACAGAUGACCGGCACUUGGA---GCA---UCAUC------------AU--CACCAGGAUGC
..((((((((..........))))))))((((...(((((((....)))))))..(((((...((.......---)).---)))))------------..--..))))..... ( -33.00)
>DroAna_CAF1 82014 106 - 1
GUGGCCGCAAAUUAAACGAAUUGUGGCUCGGCAUUUGGCAACAUUUGUUGCCACA-CUGACCAG---UUGGGAAAGUA---UCAGCAUCAUCAGCCGUGCCGGGUCAGGAAAC
((..((((((.((....)).))))((((((((((.(((((((....)))))))..-((((...(---((((.......---)))))....))))..)))))))))).))..)) ( -36.80)
>consensus
UUGGCCGCAAAUGAAACGAAUUGUGGCACAGCAUUUGGCAACAUUUGUUGCCACA_CUGACCGGCACUUGGA___GCA___GCAGCAU_AUCAUC__CAU__CACCAGGAAGC
...(((((((..........))))))).(((....(((((((....)))))))...)))...................................................... (-17.69 = -18.33 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 23,288,706 – 23,288,798
Length 92
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 73.63
Mean single sequence MFE -32.97
Consensus MFE -15.66
Energy contribution -16.55
Covariance contribution 0.89
Combinations/Pair 1.11
Mean z-score -2.30
Structure conservation index 0.48
SVM decision value 1.64
SVM RNA-class probability 0.969519
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23288706 92 + 27905053
-UC----CAAGUGCCGGUCAG-UGUGGCAACAAAUGUUGCCAAAGGCUGUGCCACAAUUCGUUUCAUUUGCGGCCAACGGGAACGG------GAACGGGUCG--AG
-..----...(((((((((..-..(((((((....)))))))..))))).).))).(((((((((.(((.((.....)).)))..)------))))))))..--.. ( -32.00)
>DroSec_CAF1 86325 102 + 1
CUGCUGCUCAGUGCCGGUCAG-UGUGGCAACAAAUGUUGCCAAA-GCUGUGCCACAAUUCGUUUCAUUUGCGGCCAACGGGAACGGGAACGAGAACGAGUCG--AG
...(.((((......((((((-(.(((((((....)))))))..-)))).)))....((((((((.(((.((.....)).)))..))))))))...)))).)--.. ( -35.70)
>DroSim_CAF1 89474 86 + 1
CUC----CAAGUGCCGGUCAG-UGUGGCAC--AAUGUUGCCAAAGGCUGUGC-AC-AUUCGUUUCAUUUGCGGCCAC--GGAACG-------GAACGGGUCG--AG
(((----...(((((((((..-..(((((.--.....)))))..))))).))-))-(((((((((..((.((....)--).)).)-------)))))))).)--)) ( -30.40)
>DroEre_CAF1 91791 82 + 1
-UG----CAAGUGCCGGUCAG-UGUGGCAACAAAUGUUGCCAAAUGCUGUGCCACAAUUCGUUUCAUUUGCGGCCCACGG------------------GUCGCAGG
-.(----(....)).((((((-(.(((((((....)))))))...)))).)))..............((((((((....)------------------))))))). ( -33.40)
>DroWil_CAF1 94419 89 + 1
-UA----CA---UCUGGUCAA-UGUGGCAACAAAUGUUGCCAG-UUCUGUGCCACAAUUCGUUUAAUUUGUGGCUAGAG--CACA---UUGAGAAGUGGACA--AG
-..----((---.((..((((-(((((((((....)))))).(-(((((.(((((((..........))))))))))))--))))---))))..))))....--.. ( -37.30)
>DroYak_CAF1 89069 88 + 1
-UC----CAAGUGCCGGUCAUCUGUGGCAACAAAUGUUGCCAAAUCCAGUGCCACAAUUCGUUUCAUUUGCGGCAAACGG-------------CAGGAGUCGCAGG
-((----(...(((((.....((((((((((....)))))))....)))((((.(((..........))).))))..)))-------------)))))........ ( -29.00)
>consensus
_UC____CAAGUGCCGGUCAG_UGUGGCAACAAAUGUUGCCAAAUGCUGUGCCACAAUUCGUUUCAUUUGCGGCCAACGG_AACG_______GAACGGGUCG__AG
............(((((((((...(((((((....)))))))....))).))).......((.......)))))................................ (-15.66 = -16.55 +   0.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 23,288,706 – 23,288,798
Length 92
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 73.63
Mean single sequence MFE -28.77
Consensus MFE -18.39
Energy contribution -18.87
Covariance contribution 0.48
Combinations/Pair 1.16
Mean z-score -1.86
Structure conservation index 0.64
SVM decision value 1.60
SVM RNA-class probability 0.966965
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23288706 92 - 27905053
CU--CGACCCGUUC------CCGUUCCCGUUGGCCGCAAAUGAAACGAAUUGUGGCACAGCCUUUGGCAACAUUUGUUGCCACA-CUGACCGGCACUUG----GA-
..--....(((...------(((.((..(((((((((((..........))))))).))))...(((((((....)))))))..-..)).)))....))----).- ( -30.20)
>DroSec_CAF1 86325 102 - 1
CU--CGACUCGUUCUCGUUCCCGUUCCCGUUGGCCGCAAAUGAAACGAAUUGUGGCACAGC-UUUGGCAACAUUUGUUGCCACA-CUGACCGGCACUGAGCAGCAG
..--......(((((((...(((.((..(((((((((((..........))))))).))))-..(((((((....)))))))..-..)).)))...)))).))).. ( -34.10)
>DroSim_CAF1 89474 86 - 1
CU--CGACCCGUUC-------CGUUCC--GUGGCCGCAAAUGAAACGAAU-GU-GCACAGCCUUUGGCAACAUU--GUGCCACA-CUGACCGGCACUUG----GAG
..--........((-------((((((--(.(((.(((.((.......))-.)-))...)))..))).)))...--(((((...-......)))))..)----)). ( -21.40)
>DroEre_CAF1 91791 82 - 1
CCUGCGAC------------------CCGUGGGCCGCAAAUGAAACGAAUUGUGGCACAGCAUUUGGCAACAUUUGUUGCCACA-CUGACCGGCACUUG----CA-
((..((..------------------.))..))..((((.((...((.(.(((((((..(((..((....))..))))))))))-.)...)).)).)))----).- ( -28.30)
>DroWil_CAF1 94419 89 - 1
CU--UGUCCACUUCUCAA---UGUG--CUCUAGCCACAAAUUAAACGAAUUGUGGCACAGAA-CUGGCAACAUUUGUUGCCACA-UUGACCAGA---UG----UA-
..--......((..((((---(((.--.....(((((((.((....)).)))))))......-..((((((....)))))))))-))))..)).---..----..- ( -27.90)
>DroYak_CAF1 89069 88 - 1
CCUGCGACUCCUG-------------CCGUUUGCCGCAAAUGAAACGAAUUGUGGCACUGGAUUUGGCAACAUUUGUUGCCACAGAUGACCGGCACUUG----GA-
........(((((-------------(((..((((((((..........))))))))(((....(((((((....)))))))))).....)))))...)----))- ( -30.70)
>consensus
CU__CGACCCGUUC_______CGUU_CCGUUGGCCGCAAAUGAAACGAAUUGUGGCACAGCAUUUGGCAACAUUUGUUGCCACA_CUGACCGGCACUUG____GA_
....((..........................(((((((..........))))))).(((....(((((((....)))))))...)))..)).............. (-18.39 = -18.87 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:17:52 2006