Locus 3088

Sequence ID	3R_DroMel_CAF1
Location	8,139,375 – 8,139,512
Length	137
Max. P	0.998699

overview

Window 8

Location	8,139,375 – 8,139,485
Length	110
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	93.13
Mean single sequence MFE	-31.80
Consensus MFE	-27.10
Energy contribution	-27.30
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.15
Structure conservation index	0.85
SVM decision value	2.34
SVM RNA-class probability	0.992666
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8139375 110 + 27905053
GAAUUGGAGGGCCGGAGGA---GGUUACUGGCCAACGAGCAGCCCAUAAACAGAGGACACAACAAAGUUGUUACAACAACAGCAUCGCCCGGUCACAAAAGUGACCAAAAUCA
((...((..((((((....---.....))))))..(((((.((((.......).)).)........(((((....))))).)).))).))((((((....))))))....)). ( -30.50)
>DroSec_CAF1 32999 113 + 1
GAAUUGGAGGGCCGGAGGAGGAUGUUACUGGCCAACGAGCAGCCCAUAAACAGAGGACACAACAAAGUUGUUACAACAACAGCAUCGCCCGGUCACAAAAGUGACCAAAAUCA
((...((..((((((..(......)..))))))..(((((.((((.......).)).)........(((((....))))).)).))).))((((((....))))))....)). ( -30.40)
>DroSim_CAF1 35382 113 + 1
GAAUUGGAGGGCAGGAGGAGGAGGUUACUGGCCAACGAGCAGCCCAUGAACAGAGGACACAACAAAGUUGUUACAACAACAGCAUCGCCCGGUCACAAAAGUGACCAAAAUCA
......((((((.((..(.(..(((.....)))..)...)..))......................((((((.....))))))...))))((((((....))))))....)). ( -30.00)
>DroEre_CAF1 32822 109 + 1
-AAUUGGAGGGCCCGCGGC---GGUUGCUGGCCAAGGAGCAGCCCAUAAACAGAGGACGCAACAAAGUUGUUACAACAACAGCAUCGCCCGGUCACAAAAGUGACCAAAAUCA
-.....((((((..((((.---(((((((........)))))))).....(....).)))......((((((.....))))))...))))((((((....))))))....)). ( -36.20)
>DroYak_CAF1 32285 110 + 1
AAAUUGGAGGGCCGGACGA---GGUUGUUGGCCAAGGAGCAUCCCAUAAACAGAGGACACAACAAAGUUGUUACAACAACAGCAUCGCCCGGUCACAAAAGUGACCAAAAUCA
......((((((..((.(.---.(((((((((......)).((((.......).))).(((((...)))))..)))))))..).))))))((((((....))))))....)). ( -31.90)
>consensus
GAAUUGGAGGGCCGGAGGA___GGUUACUGGCCAACGAGCAGCCCAUAAACAGAGGACACAACAAAGUUGUUACAACAACAGCAUCGCCCGGUCACAAAAGUGACCAAAAUCA
......((((((..........(((.....)))...((((...((.........))..........(((((....))))).)).))))))((((((....))))))....)). (-27.10 = -27.30 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	8,139,375 – 8,139,485
Length	110
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	93.13
Mean single sequence MFE	-33.80
Consensus MFE	-29.84
Energy contribution	-29.88
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.77
Structure conservation index	0.88
SVM decision value	1.88
SVM RNA-class probability	0.981104
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8139375 110 - 27905053
UGAUUUUGGUCACUUUUGUGACCGGGCGAUGCUGUUGUUGUAACAACUUUGUUGUGUCCUCUGUUUAUGGGCUGCUCGUUGGCCAGUAACC---UCCUCCGGCCCUCCAAUUC
.......((((((....))))))(((((..((.(((((....)))))...))..))))).........((((((...(..((.......))---..)..))))))........ ( -32.10)
>DroSec_CAF1 32999 113 - 1
UGAUUUUGGUCACUUUUGUGACCGGGCGAUGCUGUUGUUGUAACAACUUUGUUGUGUCCUCUGUUUAUGGGCUGCUCGUUGGCCAGUAACAUCCUCCUCCGGCCCUCCAAUUC
.......((((((....))))))(((((((((.(((((....)))))......)))))...((((....((((.......))))...))))..........))))........ ( -32.20)
>DroSim_CAF1 35382 113 - 1
UGAUUUUGGUCACUUUUGUGACCGGGCGAUGCUGUUGUUGUAACAACUUUGUUGUGUCCUCUGUUCAUGGGCUGCUCGUUGGCCAGUAACCUCCUCCUCCUGCCCUCCAAUUC
.......((((((....))))))(((((((((.(((((....)))))......)))))....(((..(((.(........).)))..)))...........))))........ ( -30.40)
>DroEre_CAF1 32822 109 - 1
UGAUUUUGGUCACUUUUGUGACCGGGCGAUGCUGUUGUUGUAACAACUUUGUUGCGUCCUCUGUUUAUGGGCUGCUCCUUGGCCAGCAACC---GCCGCGGGCCCUCCAAUU-
.......((((((....))))))(((((..((.(((((....)))))...))..)))))........((((..((.((.((((........---)))).))))..))))...- ( -37.30)
>DroYak_CAF1 32285 110 - 1
UGAUUUUGGUCACUUUUGUGACCGGGCGAUGCUGUUGUUGUAACAACUUUGUUGUGUCCUCUGUUUAUGGGAUGCUCCUUGGCCAACAACC---UCGUCCGGCCCUCCAAUUU
.......((((((....))))))((((((((..(((((((.((((....))))(((((((........)))))))........))))))).---.))))..))))........ ( -37.00)
>consensus
UGAUUUUGGUCACUUUUGUGACCGGGCGAUGCUGUUGUUGUAACAACUUUGUUGUGUCCUCUGUUUAUGGGCUGCUCGUUGGCCAGUAACC___UCCUCCGGCCCUCCAAUUC
.......((((((....))))))(((((((((.(((((....)))))......)))))....(((....((((.......))))...)))...........))))........ (-29.84 = -29.88 +   0.04)

alignment

secondary structure

dotplot

Window 0

Location	8,139,411 – 8,139,512
Length	101
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	94.32
Mean single sequence MFE	-26.18
Consensus MFE	-22.57
Energy contribution	-23.57
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-3.54
Structure conservation index	0.86
SVM decision value	3.19
SVM RNA-class probability	0.998699
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8139411 101 + 27905053
CAGCCCAUAAACAGAGGACACAACAAAGUUGUUACAACAACAGCAUCGCCCGGUCACAAAAGUGACCAAAAUCAGAGGCUACCAAAGUAGUAACAGAUGCU
...........................(((((....)))))((((((....((((((....)))))).......(..(((((....)))))..).)))))) ( -26.60)
>DroSec_CAF1 33038 101 + 1
CAGCCCAUAAACAGAGGACACAACAAAGUUGUUACAACAACAGCAUCGCCCGGUCACAAAAGUGACCAAAAUCAGAGGCUACCAAAGUAGUAACAGAUGCU
...........................(((((....)))))((((((....((((((....)))))).......(..(((((....)))))..).)))))) ( -26.60)
>DroSim_CAF1 35421 101 + 1
CAGCCCAUGAACAGAGGACACAACAAAGUUGUUACAACAACAGCAUCGCCCGGUCACAAAAGUGACCAAAAUCAGAGGCUACCAAAGUAGUAACAGAUGCU
...........................(((((....)))))((((((....((((((....)))))).......(..(((((....)))))..).)))))) ( -26.60)
>DroEre_CAF1 32857 101 + 1
CAGCCCAUAAACAGAGGACGCAACAAAGUUGUUACAACAACAGCAUCGCCCGGUCACAAAAGUGACCAAAAUCAGAGGCUACCAAAGUAGUAACAGAUGCU
..((((.........))..))......(((((....)))))((((((....((((((....)))))).......(..(((((....)))))..).)))))) ( -27.50)
>DroYak_CAF1 32321 101 + 1
CAUCCCAUAAACAGAGGACACAACAAAGUUGUUACAACAACAGCAUCGCCCGGUCACAAAAGUGACCAAAAUCAGGGGCUACCAAAGUAGUAACAGAUGCU
..((((.......).))).........(((((....)))))((((((....((((((....)))))).......(..(((((....)))))..).)))))) ( -29.70)
>DroAna_CAF1 29492 97 + 1
CAUCCCAUAAACAGAGGACACAACAAAGUUGUAGGAACAACAGGAACCUCUG----CAAAAGUGACCAAAAUCAGGGGCUACCAAAGUAGUAACAGAUGCU
...(((.....((((((..(((((...))))).(......).....))))))----......(((......))))))(((((....))))).......... ( -20.10)
>consensus
CAGCCCAUAAACAGAGGACACAACAAAGUUGUUACAACAACAGCAUCGCCCGGUCACAAAAGUGACCAAAAUCAGAGGCUACCAAAGUAGUAACAGAUGCU
...........................(((((....)))))((((((....((((((....)))))).......(..(((((....)))))..).)))))) (-22.57 = -23.57 +   1.00)

alignment

secondary structure

dotplot

Window 1

Location	8,139,411 – 8,139,512
Length	101
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	94.32
Mean single sequence MFE	-30.38
Consensus MFE	-25.61
Energy contribution	-26.67
Covariance contribution	1.06
Combinations/Pair	1.07
Mean z-score	-2.50
Structure conservation index	0.84
SVM decision value	1.43
SVM RNA-class probability	0.953529
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8139411 101 - 27905053
AGCAUCUGUUACUACUUUGGUAGCCUCUGAUUUUGGUCACUUUUGUGACCGGGCGAUGCUGUUGUUGUAACAACUUUGUUGUGUCCUCUGUUUAUGGGCUG
((((((.((((((.....)))))).......(((((((((....))))))))).))))))(((((....)))))........((((.........)))).. ( -31.20)
>DroSec_CAF1 33038 101 - 1
AGCAUCUGUUACUACUUUGGUAGCCUCUGAUUUUGGUCACUUUUGUGACCGGGCGAUGCUGUUGUUGUAACAACUUUGUUGUGUCCUCUGUUUAUGGGCUG
((((((.((((((.....)))))).......(((((((((....))))))))).))))))(((((....)))))........((((.........)))).. ( -31.20)
>DroSim_CAF1 35421 101 - 1
AGCAUCUGUUACUACUUUGGUAGCCUCUGAUUUUGGUCACUUUUGUGACCGGGCGAUGCUGUUGUUGUAACAACUUUGUUGUGUCCUCUGUUCAUGGGCUG
....................((((((.(((....((((((....))))))(((((..((.(((((....)))))...))..))))).....))).)))))) ( -31.40)
>DroEre_CAF1 32857 101 - 1
AGCAUCUGUUACUACUUUGGUAGCCUCUGAUUUUGGUCACUUUUGUGACCGGGCGAUGCUGUUGUUGUAACAACUUUGUUGCGUCCUCUGUUUAUGGGCUG
((((((.((((((.....)))))).......(((((((((....))))))))).))))))......((((((....))))))((((.........)))).. ( -33.30)
>DroYak_CAF1 32321 101 - 1
AGCAUCUGUUACUACUUUGGUAGCCCCUGAUUUUGGUCACUUUUGUGACCGGGCGAUGCUGUUGUUGUAACAACUUUGUUGUGUCCUCUGUUUAUGGGAUG
((((((...((((.....))))((((........((((((....))))))))))))))))(((((....)))))........(((((........))))). ( -32.30)
>DroAna_CAF1 29492 97 - 1
AGCAUCUGUUACUACUUUGGUAGCCCCUGAUUUUGGUCACUUUUG----CAGAGGUUCCUGUUGUUCCUACAACUUUGUUGUGUCCUCUGUUUAUGGGAUG
.......((((((.....))))))(((((((....)))).....(----((((((.....(((((....)))))..........)))))))....)))... ( -22.86)
>consensus
AGCAUCUGUUACUACUUUGGUAGCCUCUGAUUUUGGUCACUUUUGUGACCGGGCGAUGCUGUUGUUGUAACAACUUUGUUGUGUCCUCUGUUUAUGGGCUG
((((((.((((((.....)))))).......(((((((((....))))))))).))))))(((((....)))))........((((.........)))).. (-25.61 = -26.67 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:46 2006