Locus 1768

Sequence ID 3R_DroMel_CAF1
Location 5,096,813 – 5,096,972
Length 159
Max. P 0.941392
window2901 window2902 window2903

overview

Window 1

Location 5,096,813 – 5,096,932
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.41
Mean single sequence MFE -27.59
Consensus MFE -18.40
Energy contribution -18.76
Covariance contribution 0.36
Combinations/Pair 1.07
Mean z-score -2.23
Structure conservation index 0.67
SVM decision value 0.55
SVM RNA-class probability 0.779086
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5096813 119 - 27905053
CCCGAAAAACCGCAGGCAGAA-AAAACCACCAAUGGUUUUCGACUGUCAGCAAAAGCGAUUUUUAAACAACGCCCGAAAAUUGCCAAAUAAAUUCGGCUUACAGGCUACACGGCCAAGCC
.(((((.....((.(((((..-(((((((....)))))))...))))).))....(((((((((...........)))))))))........)))))......((((....))))..... ( -31.30)
>DroSec_CAF1 3940 119 - 1
CCCGAAAAACCGCAGGCCGAA-AAAACCACCAAUGGUUUUCGACUGUCAGCAAAAGCGUUUUUUAAACAACGCCCGAAAAUUGCCAAAUAAAUUCGGCUUACAGGCUACACGGCCCAGCC
...........((.(((((..-(((((((....)))))))...((((.(((....(((((........))))).((((.(((....)))...))))))).))))......)))))..)). ( -31.00)
>DroSim_CAF1 3939 119 - 1
CACGAAAAACCGCAGGCCGAA-AAAACCACCAAUGGUUUUCGACUGUCAGCAAAAGCGUUUUUUAAACAACGCCCGAAAAUUGCCAAAUAAAUUCGGCUUACAGGCUACACGGCCACGCC
...........((.(((((..-(((((((....)))))))...((((.(((....(((((........))))).((((.(((....)))...))))))).))))......)))))..)). ( -30.90)
>DroEre_CAF1 3933 103 - 1
CCCGAA-AACCGCAGGCAAA--AAACCCACCAAUGGUUUCCGACUGUCAGCAGAAGCGUUUUUUAAACAGCGGCCGAAAAUUGC-AAAUAAAUUCGGCUUACAGC-------------CC
...(((-((.(((.((....--(((((.......)))))))..(((....)))..))).))))).....(((((((((......-.......)))))))....))-------------.. ( -20.52)
>DroYak_CAF1 3987 103 - 1
CCCGAA-AACCGCAGCCAAAAAAAAACCAGCAAUGGUUUUCGACUGUCAGCAGGAGCGUUUUUUAAACAACGGCCGAAAAUUGC-AAAUAAAUUCGGCUUACAGC---------------
...(((-((.(((.........(((((((....)))))))...(((....)))..))).))))).......(((((((......-.......)))))))......--------------- ( -24.22)
>consensus
CCCGAAAAACCGCAGGCAGAA_AAAACCACCAAUGGUUUUCGACUGUCAGCAAAAGCGUUUUUUAAACAACGCCCGAAAAUUGCCAAAUAAAUUCGGCUUACAGGCUACACGGCC__GCC
..((((.(((((..((.............))..))))))))).((((.(((....(((((........))))).((((.(((....)))...))))))).))))................ (-18.40 = -18.76 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 5,096,853 – 5,096,972
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.74
Mean single sequence MFE -36.74
Consensus MFE -31.02
Energy contribution -31.06
Covariance contribution 0.04
Combinations/Pair 1.13
Mean z-score -1.75
Structure conservation index 0.84
SVM decision value 1.32
SVM RNA-class probability 0.941392
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5096853 119 + 27905053
UUUUCGGGCGUUGUUUAAAAAUCGCUUUUGCUGACAGUCGAAAACCAUUGGUGGUUUU-UUCUGCCUGCGGUUUUUCGGGCCUCAACUGCGACAUUUUCGUCCUGGCAGCAGAUGCGUUU
((((..(((...)))..)))).(((.(((((((.(((.((((((.....((..(....-..)..))(((((((...........)))))))...))))))..))).))))))).)))... ( -33.20)
>DroSec_CAF1 3980 118 + 1
UUUUCGGGCGUUGUUUAAAAAACGCUUUUGCUGACAGUCGAAAACCAUUGGUGGUUUU-UUCGGCCUGCGGUUUUUCGGG-CUCAACUGCGACAUUUUCGUCCUGGCAGCAGAUGCGUUU
...................((((((.(((((((.((((((((((((...(((.(....-..).)))...)).)))))))(-(......))(((......)))))).))))))).)))))) ( -36.10)
>DroSim_CAF1 3979 118 + 1
UUUUCGGGCGUUGUUUAAAAAACGCUUUUGCUGACAGUCGAAAACCAUUGGUGGUUUU-UUCGGCCUGCGGUUUUUCGUG-CUCAACUGCGACAUUUUCGUCCUGGCAGCAGAUGCGUUU
...................((((((.(((((((.(((.((((((.....(((.(....-..).)))(((((((.......-...)))))))...))))))..))).))))))).)))))) ( -34.90)
>DroEre_CAF1 3959 116 + 1
UUUUCGGCCGCUGUUUAAAAAACGCUUCUGCUGACAGUCGGAAACCAUUGGUGGGUUU--UUUGCCUGCGGUU-UUCGGG-CUUUACUGCGACAUUUCCCUCCUGGCAGCAGAUGCGUUU
...................((((((.(((((((.((((((((((((....(..(((..--...)))..)))))-)))))(-(......))............))).))))))).)))))) ( -40.80)
>DroYak_CAF1 4011 118 + 1
UUUUCGGCCGUUGUUUAAAAAACGCUCCUGCUGACAGUCGAAAACCAUUGCUGGUUUUUUUUUGGCUGCGGUU-UUCGGG-CUUUACUGCGACAUUUCCCUCCUGGCAGCAGAUGCGUUU
...................((((((..((((((.((((((((((((...((..(.......)..))...))))-)))))(-(......))............))).))))))..)))))) ( -38.70)
>consensus
UUUUCGGGCGUUGUUUAAAAAACGCUUUUGCUGACAGUCGAAAACCAUUGGUGGUUUU_UUCUGCCUGCGGUUUUUCGGG_CUCAACUGCGACAUUUUCGUCCUGGCAGCAGAUGCGUUU
...................((((((.(((((((.((((((((((((...((..(.......)..))...)))).)))))...........(((......)))))).))))))).)))))) (-31.02 = -31.06 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 5,096,853 – 5,096,972
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.74
Mean single sequence MFE -32.40
Consensus MFE -24.46
Energy contribution -24.78
Covariance contribution 0.32
Combinations/Pair 1.07
Mean z-score -2.27
Structure conservation index 0.75
SVM decision value 0.93
SVM RNA-class probability 0.884872
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5096853 119 - 27905053
AAACGCAUCUGCUGCCAGGACGAAAAUGUCGCAGUUGAGGCCCGAAAAACCGCAGGCAGAA-AAAACCACCAAUGGUUUUCGACUGUCAGCAAAAGCGAUUUUUAAACAACGCCCGAAAA
...(((...(((((....(((......)))((((((((.(((((......))..)))....-.((((((....)))))))))))))))))))...)))...................... ( -30.00)
>DroSec_CAF1 3980 118 - 1
AAACGCAUCUGCUGCCAGGACGAAAAUGUCGCAGUUGAG-CCCGAAAAACCGCAGGCCGAA-AAAACCACCAAUGGUUUUCGACUGUCAGCAAAAGCGUUUUUUAAACAACGCCCGAAAA
((((((...(((((....(((......)))(((((((((-((((......))..)))....-.((((((....)))))))))))))))))))...))))))................... ( -31.30)
>DroSim_CAF1 3979 118 - 1
AAACGCAUCUGCUGCCAGGACGAAAAUGUCGCAGUUGAG-CACGAAAAACCGCAGGCCGAA-AAAACCACCAAUGGUUUUCGACUGUCAGCAAAAGCGUUUUUUAAACAACGCCCGAAAA
((((((...(((((....(((......)))(((((((((-(.((......))...))....-.((((((....)))))))))))))))))))...))))))................... ( -29.20)
>DroEre_CAF1 3959 116 - 1
AAACGCAUCUGCUGCCAGGAGGGAAAUGUCGCAGUAAAG-CCCGAA-AACCGCAGGCAAA--AAACCCACCAAUGGUUUCCGACUGUCAGCAGAAGCGUUUUUUAAACAGCGGCCGAAAA
((((((.(((((((.(((..(((((.((((((.((....-......-.)).)).))))..--....(((....))))))))..))).))))))).))))))................... ( -36.10)
>DroYak_CAF1 4011 118 - 1
AAACGCAUCUGCUGCCAGGAGGGAAAUGUCGCAGUAAAG-CCCGAA-AACCGCAGCCAAAAAAAAACCAGCAAUGGUUUUCGACUGUCAGCAGGAGCGUUUUUUAAACAACGGCCGAAAA
((((((..((((((.(((..(((...((......))...-)))(((-(((((..((.............))..))))))))..))).))))))..))))))................... ( -35.42)
>consensus
AAACGCAUCUGCUGCCAGGACGAAAAUGUCGCAGUUGAG_CCCGAAAAACCGCAGGCAGAA_AAAACCACCAAUGGUUUUCGACUGUCAGCAAAAGCGUUUUUUAAACAACGCCCGAAAA
((((((.(.(((((.(((((((....))))............((((.(((((..((.............))..))))))))).))).))))).).))))))................... (-24.46 = -24.78 +   0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:50 2006