Locus 464

Sequence ID	3L_DroMel_CAF1
Location	1,335,023 – 1,335,222
Length	199
Max. P	0.963846

overview

Window 2

Location	1,335,023 – 1,335,143
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.83
Mean single sequence MFE	-41.30
Consensus MFE	-31.84
Energy contribution	-33.00
Covariance contribution	1.16
Combinations/Pair	1.15
Mean z-score	-1.83
Structure conservation index	0.77
SVM decision value	0.59
SVM RNA-class probability	0.791840
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1335023 120 + 23771897
GGAGAGCAGAAAUUUAAGCCUUUGUUUCCCUUUGCAGGAGGUGUUCGCGGAGUGUUCGACGUUGAGGACUUGGUGGAGCUGCUCCGCAAGGAGAAUGUGGACGACAUAUUCGUCUGCUAC
....((((((...................((((((.((((..((((((.((((.((((....)))).)))).)).))))..)))))))))).(((((((.....))))))).)))))).. ( -43.60)
>DroSec_CAF1 7264 120 + 1
GGAGAGCUGAAAUUAAAGUCUUUGUUUGCCUUUGCAGGAGGCGUUCGCGGAGUGUUUGACGUUGAGGACUUGGUGGAGCUGCUCCGUAAGGAGAAUGUGGACGACAUAUUCGUCUGCUAC
((((((((..(....(((((((((..((((((.....))))))..)(((..(....)..))).))))))))..)..)))).))))(((.(..(((((((.....)))))))..))))... ( -39.50)
>DroSim_CAF1 7321 120 + 1
GGAGAGCUGAAAUUAAAGUCUUUGUUUGCCUUUGCAGGAGGCGUUCGCGGAGUGUUCGACGUUGAGGACUUGGUGGAGCUGCUGCGUAAGGAGAAUGUGGACGACAUAUUCGUCUGCUAC
(((((.((........)))))))(((..(((((((((..(((.(((((.((((.((((....)))).)))).)))))))).))))).))))..)))(..(((((.....)))))..)... ( -43.20)
>DroEre_CAF1 7321 119 + 1
GGAGAGCUUCAAUUUAAGGC-UUGUGUCCCUUUGCAGGAGGCGUUCGCGGAGUGUUUGAUGUUGAGGACUUGGUGGAGCUGCUCCGCAAGGAGAAUGUGGACGACAUAUUCGUCUGCUAC
(((((((((.......))))-))...)))((((((.((((((.(((((.((((.(((......))).)))).)))))))..)))))))))).....(..(((((.....)))))..)... ( -42.40)
>DroYak_CAF1 7552 120 + 1
AGAGAGUUUCGAUUUAUGGCGUUGUUUCCCUUUGCAGGUGGAGUUCGCGGAGUUUUUGAUGUUGAGGACUUGGUUGAGCUGCUCCGAAAGGAGAAUGUGGACGAUAUAUUCGUCUGCUAC
................((((...(((..(((((...((.(.(((((((.((((((((......)))))))).).)))))).).)).)))))..)))..((((((.....)))))))))). ( -37.80)
>consensus
GGAGAGCUGAAAUUUAAGGCUUUGUUUCCCUUUGCAGGAGGCGUUCGCGGAGUGUUUGACGUUGAGGACUUGGUGGAGCUGCUCCGCAAGGAGAAUGUGGACGACAUAUUCGUCUGCUAC
....(((..........((((((((........))).))))).(((((.((((.(((......))).)))).)))))))).((((....))))...(..(((((.....)))))..)... (-31.84 = -33.00 +   1.16)

alignment

secondary structure

dotplot

Window 3

Location	1,335,063 – 1,335,183
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.25
Mean single sequence MFE	-42.98
Consensus MFE	-37.26
Energy contribution	-38.30
Covariance contribution	1.04
Combinations/Pair	1.10
Mean z-score	-1.41
Structure conservation index	0.87
SVM decision value	0.64
SVM RNA-class probability	0.808570
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1335063 120 + 23771897
GUGUUCGCGGAGUGUUCGACGUUGAGGACUUGGUGGAGCUGCUCCGCAAGGAGAAUGUGGACGACAUAUUCGUCUGCUACGUGCCGGAGAACCUGAAGUACGUUGACCACCUGGUGGUUU
...(((((.((((.((((....)))).)))).)))))....((((....))))...(..(((((.....)))))..).(((((((((.....)))..)))))).((((((...)))))). ( -43.50)
>DroSec_CAF1 7304 120 + 1
GCGUUCGCGGAGUGUUUGACGUUGAGGACUUGGUGGAGCUGCUCCGUAAGGAGAAUGUGGACGACAUAUUCGUCUGCUACGUGCCGGAGAACCUGAAGUAUGUUGACCACCUGGUAGUUU
((.(((((.((((.(((......))).)))).)))))))..((((....))))...(..(((((.....)))))..).(((((((((.....)))..))))))..(((....)))..... ( -38.30)
>DroSim_CAF1 7361 120 + 1
GCGUUCGCGGAGUGUUCGACGUUGAGGACUUGGUGGAGCUGCUGCGUAAGGAGAAUGUGGACGACAUAUUCGUCUGCUACGUGCCGGAGAACCUGAAGUAUGUUGACCACCUGGUAGUUU
((.(((((.((((.((((....)))).)))).))))))).(((((...(((.(((((((.....)))))))(((....(((((((((.....)))..)))))).)))..))).))))).. ( -39.50)
>DroEre_CAF1 7360 120 + 1
GCGUUCGCGGAGUGUUUGAUGUUGAGGACUUGGUGGAGCUGCUCCGCAAGGAGAAUGUGGACGACAUAUUCGUCUGCUACGUGCCGGAGAACCUGAAGUAUGUGGACCACCUGGUGGUCU
((.(((((.((((.(((......))).)))).)))))))..((((....))))...(..(((((.....)))))..)((((((((((.....)))..)))))))((((((...)))))). ( -46.30)
>DroYak_CAF1 7592 120 + 1
GAGUUCGCGGAGUUUUUGAUGUUGAGGACUUGGUUGAGCUGCUCCGAAAGGAGAAUGUGGACGAUAUAUUCGUCUGCUACGUGCCGGAAAACCUGAAGUAUGUGGACCACCUGGUGGUCU
.(((((((.((((((((......)))))))).).)))))).((((....))))...(..(((((.....)))))..)((((((((((.....)))..)))))))((((((...)))))). ( -47.30)
>consensus
GCGUUCGCGGAGUGUUUGACGUUGAGGACUUGGUGGAGCUGCUCCGCAAGGAGAAUGUGGACGACAUAUUCGUCUGCUACGUGCCGGAGAACCUGAAGUAUGUUGACCACCUGGUGGUUU
((.(((((.((((.(((......))).)))).)))))))..((((....))))...(..(((((.....)))))..).(((((((((.....)))..)))))).((((((...)))))). (-37.26 = -38.30 +   1.04)

alignment

secondary structure

dotplot

Window 4

Location	1,335,103 – 1,335,222
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.97
Mean single sequence MFE	-48.84
Consensus MFE	-38.74
Energy contribution	-39.58
Covariance contribution	0.84
Combinations/Pair	1.08
Mean z-score	-2.18
Structure conservation index	0.79
SVM decision value	1.26
SVM RNA-class probability	0.936740
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1335103 119 + 23771897
GCUCCGCAAGGAGAAUGUGGACGACAUAUUCGUCUGCUACGUGCCGGAGAACCUGAAGUACGUUGACCACCUGGUGGUUUGCAGUGGUCGCAGUUACCG-ACACAUGCUGUCCACCGCGG
...((((.(((.(((((((.....)))))))(((....(((((((((.....)))..)))))).)))..)))(((((...(((...((((.......))-))...)))...))))))))) ( -45.90)
>DroSec_CAF1 7344 119 + 1
GCUCCGUAAGGAGAAUGUGGACGACAUAUUCGUCUGCUACGUGCCGGAGAACCUGAAGUAUGUUGACCACCUGGUAGUUUGCAGUGGUCGCAGCUACCG-GCACAUGCUGUCCACGGCGG
.((((....))))...(..(((((.....)))))..)...(((((((((...........(((.((((((.((........))))))))))).)).)))-)))).(((((....))))). ( -48.30)
>DroSim_CAF1 7401 120 + 1
GCUGCGUAAGGAGAAUGUGGACGACAUAUUCGUCUGCUACGUGCCGGAGAACCUGAAGUAUGUUGACCACCUGGUAGUUUGCAGUGGUCGCAGCUACCGGGCACAUGCUGUCCACGGCGG
...(((((.((((((((((.....))))))).)))..)))))((((..((......(((((((.(....((((((((((.((.......)))))))))))))))))))).))..)))).. ( -47.00)
>DroEre_CAF1 7400 119 + 1
GCUCCGCAAGGAGAAUGUGGACGACAUAUUCGUCUGCUACGUGCCGGAGAACCUGAAGUAUGUGGACCACCUGGUGGUCUGCAGUGGACGCAGCUACCG-ACACAUGCUGACCACGGCGG
.((((....))))...(..(((((.....)))))..)....((((...............((..((((((...))))))..))((((...((((.....-......)))).)))))))). ( -48.80)
>DroYak_CAF1 7632 119 + 1
GCUCCGAAAGGAGAAUGUGGACGAUAUAUUCGUCUGCUACGUGCCGGAAAACCUGAAGUAUGUGGACCACCUGGUGGUCUGCAGUGGACGCAGCUACCG-GCACAUGCUGACCACGGCGG
.((((....))))...(..(((((.....)))))..)...(((((((.....(((..((.((..((((((...))))))..))....)).)))...)))-)))).(((((....))))). ( -54.20)
>consensus
GCUCCGCAAGGAGAAUGUGGACGACAUAUUCGUCUGCUACGUGCCGGAGAACCUGAAGUAUGUUGACCACCUGGUGGUUUGCAGUGGUCGCAGCUACCG_GCACAUGCUGUCCACGGCGG
.((((....))))...(..(((((.....)))))..).(((((((((.....)))..)))))).((((((...))))))(((.((((...((((............)))).)))).))). (-38.74 = -39.58 +   0.84)

alignment

secondary structure

dotplot

Window 5

Location	1,335,103 – 1,335,222
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.97
Mean single sequence MFE	-44.30
Consensus MFE	-36.02
Energy contribution	-36.82
Covariance contribution	0.80
Combinations/Pair	1.06
Mean z-score	-2.13
Structure conservation index	0.81
SVM decision value	1.56
SVM RNA-class probability	0.963846
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1335103 119 - 23771897
CCGCGGUGGACAGCAUGUGU-CGGUAACUGCGACCACUGCAAACCACCAGGUGGUCAACGUACUUCAGGUUCUCCGGCACGUAGCAGACGAAUAUGUCGUCCACAUUCUCCUUGCGGAGC
(((((((((((.((((((((-(((.((((..(((((((...........)))))))...(.....).))))..))))))))).)).(((......)))))))))........)))))... ( -46.00)
>DroSec_CAF1 7344 119 - 1
CCGCCGUGGACAGCAUGUGC-CGGUAGCUGCGACCACUGCAAACUACCAGGUGGUCAACAUACUUCAGGUUCUCCGGCACGUAGCAGACGAAUAUGUCGUCCACAUUCUCCUUACGGAGC
.....((((((.((((((((-(((.((..(((((((((...........)))))))......(....))).))))))))))).)).(((......)))))))))...((((....)))). ( -47.60)
>DroSim_CAF1 7401 120 - 1
CCGCCGUGGACAGCAUGUGCCCGGUAGCUGCGACCACUGCAAACUACCAGGUGGUCAACAUACUUCAGGUUCUCCGGCACGUAGCAGACGAAUAUGUCGUCCACAUUCUCCUUACGCAGC
.....((((((.(((((((((.((((.....(((((((...........)))))))....))))...((....))))))))).)).(((......)))))))))................ ( -40.30)
>DroEre_CAF1 7400 119 - 1
CCGCCGUGGUCAGCAUGUGU-CGGUAGCUGCGUCCACUGCAGACCACCAGGUGGUCCACAUACUUCAGGUUCUCCGGCACGUAGCAGACGAAUAUGUCGUCCACAUUCUCCUUGCGGAGC
.....((((.(.((((((.(-((...(((((((((..((..((((((...))))))..)).......((....)))).)))))))...))))))))).).))))...((((....)))). ( -44.20)
>DroYak_CAF1 7632 119 - 1
CCGCCGUGGUCAGCAUGUGC-CGGUAGCUGCGUCCACUGCAGACCACCAGGUGGUCCACAUACUUCAGGUUUUCCGGCACGUAGCAGACGAAUAUAUCGUCCACAUUCUCCUUUCGGAGC
.....(((....((((((((-(((.(((((((.....))).((((((...))))))...........))))..))))))))).)).(((((.....))))))))...((((....)))). ( -43.40)
>consensus
CCGCCGUGGACAGCAUGUGC_CGGUAGCUGCGACCACUGCAAACCACCAGGUGGUCAACAUACUUCAGGUUCUCCGGCACGUAGCAGACGAAUAUGUCGUCCACAUUCUCCUUACGGAGC
.....((((((.((((((((.(((.((((..(((((((...........)))))))...........))))..))))))))).)).(((......)))))))))...((((....)))). (-36.02 = -36.82 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:35 2006