Locus 6608

Sequence ID	2R_DroMel_CAF1
Location	20,700,431 – 20,700,589
Length	158
Max. P	0.998539

overview

Window 2

Location	20,700,431 – 20,700,549
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.11
Mean single sequence MFE	-32.88
Consensus MFE	-27.66
Energy contribution	-27.74
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-1.66
Structure conservation index	0.84
SVM decision value	0.91
SVM RNA-class probability	0.879234
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20700431 118 + 20766785
AAGGUGUGUCUAUGUCACAGCUCACAAAAUCAUUUCUGGUGUGUGU--GGGUUUGAAUAAAAAAUUUAUGCGUAAGCACUGUUGGCUGACAGGAGACAGAAUAUGGACAUGUGUCCCUUA
(((((((((((((((((.((((((((..((((....))))...)))--))))))))............(((....)))(((((..((....)).)))))..))))))))))....)))). ( -34.00)
>DroSec_CAF1 134327 117 + 1
-AGGUGUGUCUAUGUCACAGCUCACAAAAUCAUUUCUGGUGUGUGU--GGGUUUGAAUAAAAAAUUUAUGCGUAAGCACUGUUGGCUGACAGGAGACAGAAUAUGGACAUGUGUCCUUUA
-(((.((((((((((((.((((((((..((((....))))...)))--))))))))............(((....)))(((((..((....)).)))))..)))))))))....)))... ( -33.60)
>DroSim_CAF1 136869 118 + 1
AAGGUGUGUCUAUGUCACAGCUCACAAAAUCAUUUCUGGUGUGUGU--GGGUUUGAAUAAAAAAUUUAUGCGUAAGCACUGUUGGCUGACAGGAGACAGAAUAUGGACAUGUGUCCUUUA
((((.((((((((((((.((((((((..((((....))))...)))--))))))))............(((....)))(((((..((....)).)))))..)))))))))....)))).. ( -34.50)
>DroEre_CAF1 174841 113 + 1
---GUGUGCCUAUGUCACAGCUCACAAAAUCAUUUCUGGUGUGU----GGGUUUGAAUAAAAAAUUUAUGCGUUAGCACUGUUGGCUGACAGGAGACAGAAUAUGGACAUGUGUCCUUUA
---.(((.(((...(((.((((((((..((((....)))).)))----))))))))...............((((((.(....))))))))))..)))......((((....)))).... ( -29.40)
>DroYak_CAF1 139191 120 + 1
AAGGUGUGCCUAUGUCACAGCUCACAAAAUCAUUUCUGGUGUGUGUGGGGGUUUGAAUAAAAAAUUUAUGCGCUGGCGCUGUUGGCUGACAGGAGACAGAAUAUGGACAUGUGUCCUUUA
((((...((.((((((.(((((.(((..((((....))))..((((.((.((.(((((.....))))).)).)).))))))).)))))...(....)........)))))).)))))).. ( -32.90)
>consensus
AAGGUGUGUCUAUGUCACAGCUCACAAAAUCAUUUCUGGUGUGUGU__GGGUUUGAAUAAAAAAUUUAUGCGUAAGCACUGUUGGCUGACAGGAGACAGAAUAUGGACAUGUGUCCUUUA
...(..((((((((((.(((((.(((..((((....))))((((....(.((.(((((.....))))).)).)..))))))).)))))...(....).).)))))))))..)........ (-27.66 = -27.74 +   0.08)

alignment

secondary structure

dotplot

Window 3

Location	20,700,431 – 20,700,549
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.11
Mean single sequence MFE	-24.31
Consensus MFE	-23.64
Energy contribution	-23.24
Covariance contribution	-0.40
Combinations/Pair	1.08
Mean z-score	-1.85
Structure conservation index	0.97
SVM decision value	3.13
SVM RNA-class probability	0.998539
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20700431 118 - 20766785
UAAGGGACACAUGUCCAUAUUCUGUCUCCUGUCAGCCAACAGUGCUUACGCAUAAAUUUUUUAUUCAAACCC--ACACACACCAGAAAUGAUUUUGUGAGCUGUGACAUAGACACACCUU
....((((....))))......(((((..(((((((.....((((....))))...................--.((((...((....))....)))).))..))))).)))))...... ( -23.70)
>DroSec_CAF1 134327 117 - 1
UAAAGGACACAUGUCCAUAUUCUGUCUCCUGUCAGCCAACAGUGCUUACGCAUAAAUUUUUUAUUCAAACCC--ACACACACCAGAAAUGAUUUUGUGAGCUGUGACAUAGACACACCU-
....((((....))))......(((((..(((((((.....((((....))))...................--.((((...((....))....)))).))..))))).))))).....- ( -23.90)
>DroSim_CAF1 136869 118 - 1
UAAAGGACACAUGUCCAUAUUCUGUCUCCUGUCAGCCAACAGUGCUUACGCAUAAAUUUUUUAUUCAAACCC--ACACACACCAGAAAUGAUUUUGUGAGCUGUGACAUAGACACACCUU
....((((....))))......(((((..(((((((.....((((....))))...................--.((((...((....))....)))).))..))))).)))))...... ( -23.90)
>DroEre_CAF1 174841 113 - 1
UAAAGGACACAUGUCCAUAUUCUGUCUCCUGUCAGCCAACAGUGCUAACGCAUAAAUUUUUUAUUCAAACCC----ACACACCAGAAAUGAUUUUGUGAGCUGUGACAUAGGCACAC---
....((((....))))......(((((..(((((((.....((((....))))..................(----(((...((....))....)))).))..))))).)))))...--- ( -25.10)
>DroYak_CAF1 139191 120 - 1
UAAAGGACACAUGUCCAUAUUCUGUCUCCUGUCAGCCAACAGCGCCAGCGCAUAAAUUUUUUAUUCAAACCCCCACACACACCAGAAAUGAUUUUGUGAGCUGUGACAUAGGCACACCUU
....((((....))))......(((((..(((((((.....))..((((.((((((.((....(((..................)))..)).)))))).))))))))).)))))...... ( -24.97)
>consensus
UAAAGGACACAUGUCCAUAUUCUGUCUCCUGUCAGCCAACAGUGCUUACGCAUAAAUUUUUUAUUCAAACCC__ACACACACCAGAAAUGAUUUUGUGAGCUGUGACAUAGACACACCUU
....((((....))))......(((((..((((.....(((((((....))..........................((((.((....))....)))).))))))))).)))))...... (-23.64 = -23.24 +  -0.40)

alignment

secondary structure

dotplot

Window 4

Location	20,700,471 – 20,700,589
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.29
Mean single sequence MFE	-27.42
Consensus MFE	-24.76
Energy contribution	-24.52
Covariance contribution	-0.24
Combinations/Pair	1.04
Mean z-score	-1.18
Structure conservation index	0.90
SVM decision value	0.16
SVM RNA-class probability	0.612803
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20700471 118 + 20766785
GUGUGU--GGGUUUGAAUAAAAAAUUUAUGCGUAAGCACUGUUGGCUGACAGGAGACAGAAUAUGGACAUGUGUCCCUUAUAACAACUGACAGAAGCGUAUAGCUUGAGUAUAAAAAGUU
..((((--((((((.......))))))))))(((..(.((((..(.((...(....).......((((....)))).......)).)..))))((((.....)))))..)))........ ( -26.50)
>DroSec_CAF1 134366 118 + 1
GUGUGU--GGGUUUGAAUAAAAAAUUUAUGCGUAAGCACUGUUGGCUGACAGGAGACAGAAUAUGGACAUGUGUCCUUUAUAACAACUGACAGAAGCGUAUAGCUUGAGUAUAAAAAGUU
..((((--((((((.......))))))))))(((..(.((((..(.((...(....).......((((....)))).......)).)..))))((((.....)))))..)))........ ( -26.90)
>DroSim_CAF1 136909 118 + 1
GUGUGU--GGGUUUGAAUAAAAAAUUUAUGCGUAAGCACUGUUGGCUGACAGGAGACAGAAUAUGGACAUGUGUCCUUUAUAACAACUGACAGAAGCGUAUAGCUUGAGUAUAAAAAGUU
..((((--((((((.......))))))))))(((..(.((((..(.((...(....).......((((....)))).......)).)..))))((((.....)))))..)))........ ( -26.90)
>DroEre_CAF1 174878 116 + 1
GUGU----GGGUUUGAAUAAAAAAUUUAUGCGUUAGCACUGUUGGCUGACAGGAGACAGAAUAUGGACAUGUGUCCUUUAUAACAACUGACAGAAGCGCAUAGUUUGGGUAUAAAAAGUU
....----((.(((..(((...((.(((((((((....((((..(.((...(....).......((((....)))).......)).)..)))).))))))))).))...)))..))).)) ( -26.00)
>DroYak_CAF1 139231 120 + 1
GUGUGUGGGGGUUUGAAUAAAAAAUUUAUGCGCUGGCGCUGUUGGCUGACAGGAGACAGAAUAUGGACAUGUGUCCUUUAUAACAACUGACAGAAGCGCAUAGUUUGGGUAUAAAAAGUU
........((.(((..(((...((.(((((((((....((((..(.((...(....).......((((....)))).......)).)..)))).))))))))).))...)))..))).)) ( -30.80)
>consensus
GUGUGU__GGGUUUGAAUAAAAAAUUUAUGCGUAAGCACUGUUGGCUGACAGGAGACAGAAUAUGGACAUGUGUCCUUUAUAACAACUGACAGAAGCGUAUAGCUUGAGUAUAAAAAGUU
........................(((((((.......((((..(.((...(....).......((((....)))).......)).)..))))((((.....))))..)))))))..... (-24.76 = -24.52 +  -0.24)

alignment

secondary structure

dotplot

Window 5

Location	20,700,471 – 20,700,589
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.29
Mean single sequence MFE	-19.02
Consensus MFE	-15.08
Energy contribution	-14.92
Covariance contribution	-0.16
Combinations/Pair	1.06
Mean z-score	-1.57
Structure conservation index	0.79
SVM decision value	-0.04
SVM RNA-class probability	0.514700
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20700471 118 - 20766785
AACUUUUUAUACUCAAGCUAUACGCUUCUGUCAGUUGUUAUAAGGGACACAUGUCCAUAUUCUGUCUCCUGUCAGCCAACAGUGCUUACGCAUAAAUUUUUUAUUCAAACCC--ACACAC
..........((..((((.....))))..))..((((.......((((....)))).....(((.(....).))).)))).((((....))))...................--...... ( -17.20)
>DroSec_CAF1 134366 118 - 1
AACUUUUUAUACUCAAGCUAUACGCUUCUGUCAGUUGUUAUAAAGGACACAUGUCCAUAUUCUGUCUCCUGUCAGCCAACAGUGCUUACGCAUAAAUUUUUUAUUCAAACCC--ACACAC
..........((..((((.....))))..))..((((.......((((....)))).....(((.(....).))).)))).((((....))))...................--...... ( -17.40)
>DroSim_CAF1 136909 118 - 1
AACUUUUUAUACUCAAGCUAUACGCUUCUGUCAGUUGUUAUAAAGGACACAUGUCCAUAUUCUGUCUCCUGUCAGCCAACAGUGCUUACGCAUAAAUUUUUUAUUCAAACCC--ACACAC
..........((..((((.....))))..))..((((.......((((....)))).....(((.(....).))).)))).((((....))))...................--...... ( -17.40)
>DroEre_CAF1 174878 116 - 1
AACUUUUUAUACCCAAACUAUGCGCUUCUGUCAGUUGUUAUAAAGGACACAUGUCCAUAUUCUGUCUCCUGUCAGCCAACAGUGCUAACGCAUAAAUUUUUUAUUCAAACCC----ACAC
..................((((((...((((..((((......((((.(((.(........)))).))))..))))..))))......))))))..................----.... ( -19.00)
>DroYak_CAF1 139231 120 - 1
AACUUUUUAUACCCAAACUAUGCGCUUCUGUCAGUUGUUAUAAAGGACACAUGUCCAUAUUCUGUCUCCUGUCAGCCAACAGCGCCAGCGCAUAAAUUUUUUAUUCAAACCCCCACACAC
..................((((((((.......((((((.....((((....)))).....(((.(....).)))..))))))...)))))))).......................... ( -24.10)
>consensus
AACUUUUUAUACUCAAGCUAUACGCUUCUGUCAGUUGUUAUAAAGGACACAUGUCCAUAUUCUGUCUCCUGUCAGCCAACAGUGCUUACGCAUAAAUUUUUUAUUCAAACCC__ACACAC
.......................((..((((..((((......((((.(((.(........)))).))))..))))..)))).))................................... (-15.08 = -14.92 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:57 2006