Locus 3357

Sequence ID	3L_DroMel_CAF1
Location	9,825,027 – 9,825,251
Length	224
Max. P	0.994968

overview

Window 0

Location	9,825,027 – 9,825,124
Length	97
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	97.13
Mean single sequence MFE	-35.18
Consensus MFE	-32.92
Energy contribution	-32.44
Covariance contribution	-0.48
Combinations/Pair	1.10
Mean z-score	-1.84
Structure conservation index	0.94
SVM decision value	2.34
SVM RNA-class probability	0.992604
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9825027 97 - 23771897
CUUGACCUCCUCGCAUUUACUUUGAUGUUGUUGACUUCAU-CAGGGGUCAGAGGCAUCUGUGGAACACCGGGUGGGUCAGUUGUCGUCCGGAUCGAGU
.((((((..((((..(((((...(((((..((((((((..-..))))))))..))))).)))))....))))..))))))...(((.......))).. ( -34.20)
>DroSec_CAF1 119051 97 - 1
CUUGACCUCUUCGCAUUUACUUUGAUGUUGUUGACUUCAU-CAGGGGUCAGAGGCAUCUGUGGAACACCGGGUGGGUCAGUUGUCGUCCGGAUCGGAU
.(((((((.((((..(((((...(((((..((((((((..-..))))))))..))))).)))))....)))).))))))).....(((((...))))) ( -34.10)
>DroSim_CAF1 122313 97 - 1
CUUGACCUCCUCGCAUUUACUUUGAUGUUGUUGACUUCAU-CAGGGGUCAGAGGCAUCUGUGGAACACCGGGUGGGUCAGUUGUCGUCCGGAUCGGAU
.((((((..((((..(((((...(((((..((((((((..-..))))))))..))))).)))))....))))..)))))).....(((((...))))) ( -36.90)
>DroEre_CAF1 121885 97 - 1
CUUGACCUCCUCGCAUUUACUUUGAUGUUGUUGACUUCAU-CAGGGGUCAGAGGCAUCUGUGGAACACCGGGUGGGUCAGUUGUCGCGCGGAUCGGAU
.((((((..((((..(((((...(((((..((((((((..-..))))))))..))))).)))))....))))..))))))..(((.((.....))))) ( -33.60)
>DroYak_CAF1 132094 98 - 1
CUUGACCUCCUCGCAUUUGCUUUGAUGUUGUUGACUUCAUUCAGGGGUCAGAGGCAUCUGUGGAACACCGGGUGGGUCAGUUGUCGUCCGGAUCGGAU
.((((((..((((..((..(...(((((..((((((((.....))))))))..))))).)..))....))))..)))))).....(((((...))))) ( -37.10)
>consensus
CUUGACCUCCUCGCAUUUACUUUGAUGUUGUUGACUUCAU_CAGGGGUCAGAGGCAUCUGUGGAACACCGGGUGGGUCAGUUGUCGUCCGGAUCGGAU
.((((((..((((..(((((...(((((..((((((((.....))))))))..))))).)))))....))))..))))))...(((.......))).. (-32.92 = -32.44 +  -0.48)

alignment

secondary structure

dotplot

Window 1

Location	9,825,045 – 9,825,151
Length	106
Sequences	4
Columns	113
Reading direction	reverse
Mean pairwise identity	91.44
Mean single sequence MFE	-34.08
Consensus MFE	-32.94
Energy contribution	-32.75
Covariance contribution	-0.19
Combinations/Pair	1.04
Mean z-score	-1.26
Structure conservation index	0.97
SVM decision value	0.12
SVM RNA-class probability	0.594077
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9825045 106 - 23771897
GGGGGGG---GCU---UUUUUUAUGACUUAACGCUUGACCUCCUCGCAUUUACUUUGAUGUUGUUGACUUCAU-CAGGGGUCAGAGGCAUCUGUGGAACACCGGGUGGGUCAG
(.(..((---((.---........).)))..).).(((((..((((..(((((...(((((..((((((((..-..))))))))..))))).)))))....))))..))))). ( -34.60)
>DroSim_CAF1 122331 109 - 1
GGAUGGGGAGCCC---UUUUUUAUGACUUAACGCUUGACCUCCUCGCAUUUACUUUGAUGUUGUUGACUUCAU-CAGGGGUCAGAGGCAUCUGUGGAACACCGGGUGGGUCAG
....(((....))---)..................(((((..((((..(((((...(((((..((((((((..-..))))))))..))))).)))))....))))..))))). ( -35.50)
>DroEre_CAF1 121903 101 - 1
G--------GCCC---UUUUUUAUGACUUAACGCUUGACCUCCUCGCAUUUACUUUGAUGUUGUUGACUUCAU-CAGGGGUCAGAGGCAUCUGUGGAACACCGGGUGGGUCAG
.--------....---...................(((((..((((..(((((...(((((..((((((((..-..))))))))..))))).)))))....))))..))))). ( -33.00)
>DroYak_CAF1 132112 105 - 1
G--------GCCCCUUUUUUUUAUGACUUAACGCUUGACCUCCUCGCAUUUGCUUUGAUGUUGUUGACUUCAUUCAGGGGUCAGAGGCAUCUGUGGAACACCGGGUGGGUCAG
.--------..........................(((((..((((..((..(...(((((..((((((((.....))))))))..))))).)..))....))))..))))). ( -33.20)
>consensus
G________GCCC___UUUUUUAUGACUUAACGCUUGACCUCCUCGCAUUUACUUUGAUGUUGUUGACUUCAU_CAGGGGUCAGAGGCAUCUGUGGAACACCGGGUGGGUCAG
...................................(((((..((((..(((((...(((((..((((((((.....))))))))..))))).)))))....))))..))))). (-32.94 = -32.75 +  -0.19)

alignment

secondary structure

dotplot

Window 2

Location	9,825,151 – 9,825,251
Length	100
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.87
Mean single sequence MFE	-28.20
Consensus MFE	-24.17
Energy contribution	-24.81
Covariance contribution	0.64
Combinations/Pair	1.09
Mean z-score	-2.49
Structure conservation index	0.86
SVM decision value	2.53
SVM RNA-class probability	0.994968
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9825151 100 + 23771897
CCCCUA-------AAAA-------------GGGAAAAAUGGGGAAAUGCGAGUAUGUAUAACAUUAUAACAUGCUGCUGCCUCAUUGUGGAAAGCCACAGAUAAAUGUUAAUCAUCACAG
.((((.-------...)-------------)))...(((((((....((.((((((((((....))).)))))))))..)))))))((((....)))).(((........)))....... ( -27.90)
>DroSec_CAF1 119185 113 + 1
CCCCUA-------AAAAUAAAAAAUGGAUGGGGGAAAAUGGGGAAAUGCGAGUAUGUAUAACAUUAUAACAUGCUGCUGCCUCAUUGUGGAAAGCCACAGAUAAAUGUUAAUCAUCGCAG
((((((-------...((.....))...))))))..(((((((....((.((((((((((....))).)))))))))..)))))))((((....)))).(((........)))....... ( -30.70)
>DroSim_CAF1 122440 113 + 1
CCCUUA-------AAAAGAAAAAAUGGAUGGGGGAAAAUGGGGAAAUGCGAGUAUGUAUAACAUUAUAACAUGCUGCUGCAUCAUUGUGGAAAGCCACAGAUAAAUGUUAAUCAUCGCAG
((((((-------...............))))))............(((((...((..(((((((.....((((....))))..((((((....))))))...)))))))..))))))). ( -25.26)
>DroEre_CAF1 122004 120 + 1
CCCCUACAAAAAAAAAAAAAAAAAUGGCUAGGGGAAAAUGGGGAAAUGCGAGUAUGUAUAACAUUAUGACAUGCUGCUGCCUCAUUGUGGAAAGCCAGAGAUAAAUGUUAAUCAUCGCUG
((((((......................))))))..(((((((....((.((((((((((....))).)))))))))..))))))).(((....)))(((((........))).)).... ( -27.45)
>DroYak_CAF1 132217 110 + 1
CCCCUA----------AAAAAAAAUUGGUAGGGGAAAAUGGGGAAAUGCCAGUAUGUAUAACAUUAUGGCAUGCUGCUGCCUCAUUGUGGAAAGCCAGAGAUAAAUGUUAAUCAUCGCGG
((((((----------..((....))..))))))..(((((((....((.((((((((((....))).)))))))))..))))))).(((....)))(((((........))).)).... ( -29.70)
>consensus
CCCCUA_______AAAAAAAAAAAUGGAUAGGGGAAAAUGGGGAAAUGCGAGUAUGUAUAACAUUAUAACAUGCUGCUGCCUCAUUGUGGAAAGCCACAGAUAAAUGUUAAUCAUCGCAG
((((((......................))))))..(((((((....((.((((((((((....)))).))))))))..)))))))((((....)))).(((........)))....... (-24.17 = -24.81 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:03 2006