Locus 8867

Sequence ID	3R_DroMel_CAF1
Location	23,807,061 – 23,807,196
Length	135
Max. P	0.962916

overview

Window 2

Location	23,807,061 – 23,807,157
Length	96
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	80.04
Mean single sequence MFE	-32.73
Consensus MFE	-14.74
Energy contribution	-15.93
Covariance contribution	1.20
Combinations/Pair	1.18
Mean z-score	-2.53
Structure conservation index	0.45
SVM decision value	0.29
SVM RNA-class probability	0.668306
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23807061 96 + 27905053
UGUGUUAGGUGUGUGAG----CGCAUGUGGUGCUAAAUGGCAAGUGGAUGCCACAACCACCUGAAUUGGCGUUGGAGCAUCUGAGCCAUCAAAGAAAUUA
.(..(((.(((((....----))))).)))..)...(((((...(((((((..((((..((......)).))))..))))))).)))))........... ( -32.50)
>DroSec_CAF1 12354 94 + 1
UCUGUUUAG-GAGUGAG----CGCAUGUGGUGCUAAAUGGCAAGUGGAUGCCACAAC-UCCUGAAUUGGCGAUGGAGCAUCUGAGCCAUCAAAGAAAUUA
(((((((((-((((.((----(((.....)))))...(((((......)))))..))-))))))))....(((((..(....)..)))))..)))..... ( -33.40)
>DroSim_CAF1 12397 95 + 1
UGUGUUAAG-GAGUGAG----CGCAUGUGGUGCUAAAUGGCAAGUGGAUGCCACAACCACCUGAAUUGGCGAUGGAGCAUCUGAGCCAUCAAAGAAAUUA
.........-..((.((----..((.((((((((....)))..((((...)))).))))).))..)).))(((((..(....)..))))).......... ( -25.90)
>DroEre_CAF1 12601 91 + 1
---GUUAA--GCGUGAG----CGCAUGUGGUGCUAAAUGGCAAGUGGAUGCCACCACCACCUGAAUUGGCGGUGGAGCAUCUGAGCCAUCAAAGAAAUUA
---.....--((....)----)((((...))))...(((((...(((((((..(((((.((......)).))))).))))))).)))))........... ( -34.50)
>DroYak_CAF1 12904 95 + 1
---GUUAG--GCGUGAGCGGGCGCAUGUGGUGCUAAAUGGCAAGUGGAUGCCACAACCACCUGAAUUGGCGGUGGAGCAUCUGAGCCACCAAAGAAAUUA
---.....--((....))((((((.....))))....((((...(((((((..((.((.((......)).))))..))))))).)))))).......... ( -33.90)
>DroPer_CAF1 12431 89 + 1
---GUGCG--GCAUCA------CCAUGUGGCAUCAAACGGCAAGUACCUGCCCCCUCCACCCGUUGGGGGGCAGGGCCAUCUGAGGCAAAAGCGAAACCA
---((((.--((((..------..)))).))))......((.....((((((((((.........))))))))))(((......)))....))....... ( -36.20)
>consensus
___GUUAA__GCGUGAG____CGCAUGUGGUGCUAAAUGGCAAGUGGAUGCCACAACCACCUGAAUUGGCGAUGGAGCAUCUGAGCCAUCAAAGAAAUUA
......................((....((((.....(((((......)))))....)))).......))(((((..(....)..))))).......... (-14.74 = -15.93 +   1.20)

alignment

secondary structure

dotplot

Window 3

Location	23,807,061 – 23,807,157
Length	96
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	80.04
Mean single sequence MFE	-30.35
Consensus MFE	-17.77
Energy contribution	-18.72
Covariance contribution	0.95
Combinations/Pair	1.32
Mean z-score	-3.05
Structure conservation index	0.59
SVM decision value	1.55
SVM RNA-class probability	0.962916
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23807061 96 - 27905053
UAAUUUCUUUGAUGGCUCAGAUGCUCCAACGCCAAUUCAGGUGGUUGUGGCAUCCACUUGCCAUUUAGCACCACAUGCG----CUCACACACCUAACACA
..........((((((...(((((..(((((((......))).))))..))))).....))))))..(((.....))).----................. ( -25.60)
>DroSec_CAF1 12354 94 - 1
UAAUUUCUUUGAUGGCUCAGAUGCUCCAUCGCCAAUUCAGGA-GUUGUGGCAUCCACUUGCCAUUUAGCACCACAUGCG----CUCACUC-CUAAACAGA
.......((((.((((...((((...))))))))....((((-((.((((((......))))))...(((.....))).----...))))-))...)))) ( -24.30)
>DroSim_CAF1 12397 95 - 1
UAAUUUCUUUGAUGGCUCAGAUGCUCCAUCGCCAAUUCAGGUGGUUGUGGCAUCCACUUGCCAUUUAGCACCACAUGCG----CUCACUC-CUUAACACA
..........((((((...(((((..(((((((......))))).))..))))).....))))))..(((.....))).----.......-......... ( -25.40)
>DroEre_CAF1 12601 91 - 1
UAAUUUCUUUGAUGGCUCAGAUGCUCCACCGCCAAUUCAGGUGGUGGUGGCAUCCACUUGCCAUUUAGCACCACAUGCG----CUCACGC--UUAAC---
..........((((((...((((((((((((((......)))))))).)))))).....))))))..(((.....)))(----(....))--.....--- ( -34.00)
>DroYak_CAF1 12904 95 - 1
UAAUUUCUUUGGUGGCUCAGAUGCUCCACCGCCAAUUCAGGUGGUUGUGGCAUCCACUUGCCAUUUAGCACCACAUGCGCCCGCUCACGC--CUAAC---
..........((((((...(((((..(((((((......))))).))..))))).....))).....(((.....)))..........))--)....--- ( -28.30)
>DroPer_CAF1 12431 89 - 1
UGGUUUCGCUUUUGCCUCAGAUGGCCCUGCCCCCCAACGGGUGGAGGGGGCAGGUACUUGCCGUUUGAUGCCACAUGG------UGAUGC--CGCAC---
.(((.(((((...((.(((((((((((((((((((........).))))))))).....))))))))).)).....))------))).))--)....--- ( -44.50)
>consensus
UAAUUUCUUUGAUGGCUCAGAUGCUCCACCGCCAAUUCAGGUGGUUGUGGCAUCCACUUGCCAUUUAGCACCACAUGCG____CUCACGC__CUAAC___
..........((((((...((((((.(((((((......)))))).).)))))).....))))))..(((.....)))...................... (-17.77 = -18.72 +   0.95)

alignment

secondary structure

dotplot

Window 4

Location	23,807,087 – 23,807,196
Length	109
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	79.07
Mean single sequence MFE	-30.26
Consensus MFE	-18.33
Energy contribution	-18.50
Covariance contribution	0.17
Combinations/Pair	1.40
Mean z-score	-2.61
Structure conservation index	0.61
SVM decision value	1.50
SVM RNA-class probability	0.959516
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23807087 109 - 27905053
UCUG-CCCAUCUCGCUAACCUCGAACCAACGAUCCUGUCUUAAUUUCUUUGAUGGCUCAGAUGCUCCAACGCCAAUUCAGGUGGUUGUGGCAUCCACUUGCCAUUUAGCA
....-........((((...(((......)))..................((((((...(((((..(((((((......))).))))..))))).....)))))))))). ( -29.10)
>DroPse_CAF1 12361 102 - 1
CCCGCUUCACUUCACUGCCUUG---CCCUCGUUUC-----UGGUUUCGCUUUUGCCUCAGAUGGCCCUGCCCCCCAACGGGUGGAGGGGGCAGGUACUUGCCGUUUGAUG
................((...(---((........-----.)))...)).......(((((((((((((((((((........).))))))))).....))))))))).. ( -34.30)
>DroSec_CAF1 12379 105 - 1
UCUG-CCCAUUUCGCUACCCUC---CCAACGAACCUGUCUUAAUUUCUUUGAUGGCUCAGAUGCUCCAUCGCCAAUUCAGGA-GUUGUGGCAUCCACUUGCCAUUUAGCA
....-........((((.....---.((((...((((..((((.....))))((((...((((...))))))))...)))).-))))(((((......)))))..)))). ( -24.40)
>DroSim_CAF1 12422 105 - 1
UCUG-CCCAAUUCGCUAC-CUC---CCAACGAACCUGUCUUAAUUUCUUUGAUGGCUCAGAUGCUCCAUCGCCAAUUCAGGUGGUUGUGGCAUCCACUUGCCAUUUAGCA
....-........((((.-...---.(((.(((...........))).)))(((((...(((((..(((((((......))))).))..))))).....))))).)))). ( -27.00)
>DroEre_CAF1 12622 106 - 1
UCUG-CCCAUUUCGCUGCCUUG---CCAUCUAACCUGUCUUAAUUUCUUUGAUGGCUCAGAUGCUCCACCGCCAAUUCAGGUGGUGGUGGCAUCCACUUGCCAUUUAGCA
....-........((((....(---(((((....................))))))...((((((((((((((......)))))))).))))))...........)))). ( -36.35)
>DroYak_CAF1 12929 106 - 1
ACUG-CCCAUUUCGCUACCUUC---CCAUCUAAAAUGUCUUAAUUUCUUUGGUGGCUCAGAUGCUCCACCGCCAAUUCAGGUGGUUGUGGCAUCCACUUGCCAUUUAGCA
....-........((((.....---(((....((((......))))...)))((((...(((((..(((((((......))))).))..))))).....))))..)))). ( -30.40)
>consensus
UCUG_CCCAUUUCGCUACCCUC___CCAACGAACCUGUCUUAAUUUCUUUGAUGGCUCAGAUGCUCCACCGCCAAUUCAGGUGGUUGUGGCAUCCACUUGCCAUUUAGCA
.............((((......................((((.....))))((((...((((((.(((((((......)))))).).)))))).....))))..)))). (-18.33 = -18.50 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:21:38 2006