Locus 4861

Sequence ID	3L_DroMel_CAF1
Location	13,599,439 – 13,599,609
Length	170
Max. P	0.999737

overview

Window 9

Location	13,599,439 – 13,599,558
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	89.02
Mean single sequence MFE	-34.53
Consensus MFE	-28.83
Energy contribution	-29.52
Covariance contribution	0.68
Combinations/Pair	1.15
Mean z-score	-3.71
Structure conservation index	0.83
SVM decision value	2.23
SVM RNA-class probability	0.990819
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13599439 119 - 23771897
AACCCAUAUAUUCAUAAUUAAUUGUUUGCCUGAGCAGACUUCUAAGUGAAUUUUCGUUCCCUUAUUAAUGGCCCACUACCUCGGGCCGUCUGCUUUGGCCCG-AAUGGCUAAUUAAACAU
..............((((((.(..((((((.((((((((...((((.((((....)))).)))).....(((((........))))))))))))).)))..)-))..).))))))..... ( -38.00)
>DroSec_CAF1 6277 120 - 1
AACCCAUAUAUUCAUAAUUAAUUGUUUGCCUGAGCAGACUUCUAAGUGAAUUUUCGUUCCCUUAUUAAUGGCCCACUACCUCGGGCCGUCUGCUUUGGCCCGGAAUGGCUAAUUAAACAU
..............((((((.(..((((((.((((((((...((((.((((....)))).)))).....(((((........))))))))))))).)))...)))..).))))))..... ( -37.60)
>DroSim_CAF1 15632 120 - 1
AACCCAUAUAUUCAUAAUUAAUUGUUUGCCUGAGCAGACUUCUAAGUGAAUUUUCGUUCCCUUAUUAAUGGCCCACUACCUCGGGCCGUCUGCUUUGGCCCGGAAUGGCUAAUUAAACAU
..............((((((.(..((((((.((((((((...((((.((((....)))).)))).....(((((........))))))))))))).)))...)))..).))))))..... ( -37.60)
>DroEre_CAF1 7489 106 - 1
AACCCACAUAUUCAUAAUUAAUUGUUUGCCUGAGCAGACUUCUAAGUGAAUUUGCGUUCCCUUAUUAAUG-------------GGCCGUCUGUUCUGGCCCG-AAUGGCUAAUUAAACAU
..............((((((.(..((((((.(((((((((((.....)))........(((........)-------------))..)))))))).)))..)-))..).))))))..... ( -26.70)
>DroYak_CAF1 12448 119 - 1
AACCCACAUAUUCAUAAUUAAUUGUUUGCCCGAGCAGACUUCUAAGUGAAUUUUCGUUCCCUUAUUAAUGGCCCACUACCUCGGGCCGUCUGCUUUGGCCCG-AAUGGCUAAUUAAACAU
..............((((((.(..((((((.((((((((...((((.((((....)))).)))).....(((((........))))))))))))).)))..)-))..).))))))..... ( -38.00)
>DroAna_CAF1 42078 117 - 1
GGCCCACAUAUCCAUUAUUAAUUGUCUUCCUGGGCAGACUUCUAAGUGAAUU-UCGUUCCCUUAUUAAUGACAGGCCGCCUCGGGCUGUCUGUUCUGGUCUG-AGUGGCUAAUUAAACA-
((((.((...((((................))))((((((..((((.((((.-..)))).)))).....(((((.(((...))).)))))......))))))-.)))))).........- ( -29.29)
>consensus
AACCCACAUAUUCAUAAUUAAUUGUUUGCCUGAGCAGACUUCUAAGUGAAUUUUCGUUCCCUUAUUAAUGGCCCACUACCUCGGGCCGUCUGCUUUGGCCCG_AAUGGCUAAUUAAACAU
..............((((((.(..((.(((.((((((((...((((.((((....)))).)))).....(((((........))))))))))))).)))....))..).))))))..... (-28.83 = -29.52 +   0.68)

alignment

secondary structure

dotplot

Window 0

Location	13,599,518 – 13,599,609
Length	91
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.74
Mean single sequence MFE	-25.28
Consensus MFE	-24.24
Energy contribution	-23.68
Covariance contribution	-0.56
Combinations/Pair	1.12
Mean z-score	-2.76
Structure conservation index	0.96
SVM decision value	3.98
SVM RNA-class probability	0.999737
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13599518 91 + 23771897
AGUCUGCUCAGGCAAACAAUUAAUUAUGAAUAUAUGGGUUAAUGGAAAACCCAGACUGAUUUUCCAGACAAAGUGCUAUUCAGCGCUUUAA-----------------------------
.(((((.((((.....((........))......((((((.......))))))..)))).....)))))((((((((....))))))))..----------------------------- ( -23.70)
>DroSec_CAF1 6357 91 + 1
AGUCUGCUCAGGCAAACAAUUAAUUAUGAAUAUAUGGGUUAAUGGAAAACCCAGACUGAUUUUCCAGACAAAGUGCUAUUCAGCGCUUUAA-----------------------------
.(((((.((((.....((........))......((((((.......))))))..)))).....)))))((((((((....))))))))..----------------------------- ( -23.70)
>DroSim_CAF1 15712 91 + 1
AGUCUGCUCAGGCAAACAAUUAAUUAUGAAUAUAUGGGUUAAUGGAAAACCCAGACUGAUUUUCCAGACAAAGUGCUAUUCAGCGCUUUAA-----------------------------
.(((((.((((.....((........))......((((((.......))))))..)))).....)))))((((((((....))))))))..----------------------------- ( -23.70)
>DroEre_CAF1 7555 120 + 1
AGUCUGCUCAGGCAAACAAUUAAUUAUGAAUAUGUGGGUUAAUGGAAAGCCCAGACUGAUUUUCCAGACAAAGUGCUAUUCAGCACUUUAAUAUUUUUGACGGAAAAUCGGGAAAACGAC
.((.(((....))).))...............(.((((((.......)))))).)((((((((((....((((((((....))))))))..((....))..))))))))))......... ( -31.80)
>DroYak_CAF1 12527 91 + 1
AGUCUGCUCGGGCAAACAAUUAAUUAUGAAUAUGUGGGUUAAUGGAAAACCCAGACUGAUUUUCCAGACAAAGUGCUAUUCAGCACUUUAA-----------------------------
.(((((.((((.....((........))....(.((((((.......)))))).))))).....)))))((((((((....))))))))..----------------------------- ( -23.50)
>consensus
AGUCUGCUCAGGCAAACAAUUAAUUAUGAAUAUAUGGGUUAAUGGAAAACCCAGACUGAUUUUCCAGACAAAGUGCUAUUCAGCGCUUUAA_____________________________
.(((((.((((.....((........))......((((((.......))))))..)))).....)))))((((((((....))))))))............................... (-24.24 = -23.68 +  -0.56)

alignment

secondary structure

dotplot

Window 1

Location	13,599,518 – 13,599,609
Length	91
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.74
Mean single sequence MFE	-23.85
Consensus MFE	-20.52
Energy contribution	-20.72
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.38
Structure conservation index	0.86
SVM decision value	2.33
SVM RNA-class probability	0.992401
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13599518 91 - 23771897
-----------------------------UUAAAGCGCUGAAUAGCACUUUGUCUGGAAAAUCAGUCUGGGUUUUCCAUUAACCCAUAUAUUCAUAAUUAAUUGUUUGCCUGAGCAGACU
-----------------------------.(((((.(((....))).)))))..(((((((((......))))))))).........................((((((....)))))). ( -21.50)
>DroSec_CAF1 6357 91 - 1
-----------------------------UUAAAGCGCUGAAUAGCACUUUGUCUGGAAAAUCAGUCUGGGUUUUCCAUUAACCCAUAUAUUCAUAAUUAAUUGUUUGCCUGAGCAGACU
-----------------------------.(((((.(((....))).)))))..(((((((((......))))))))).........................((((((....)))))). ( -21.50)
>DroSim_CAF1 15712 91 - 1
-----------------------------UUAAAGCGCUGAAUAGCACUUUGUCUGGAAAAUCAGUCUGGGUUUUCCAUUAACCCAUAUAUUCAUAAUUAAUUGUUUGCCUGAGCAGACU
-----------------------------.(((((.(((....))).)))))..(((((((((......))))))))).........................((((((....)))))). ( -21.50)
>DroEre_CAF1 7555 120 - 1
GUCGUUUUCCCGAUUUUCCGUCAAAAAUAUUAAAGUGCUGAAUAGCACUUUGUCUGGAAAAUCAGUCUGGGCUUUCCAUUAACCCACAUAUUCAUAAUUAAUUGUUUGCCUGAGCAGACU
(((........(((((((((..........(((((((((....)))))))))..))))))))).((..((((...(.(((((...............))))).)...))))..)).))). ( -29.36)
>DroYak_CAF1 12527 91 - 1
-----------------------------UUAAAGUGCUGAAUAGCACUUUGUCUGGAAAAUCAGUCUGGGUUUUCCAUUAACCCACAUAUUCAUAAUUAAUUGUUUGCCCGAGCAGACU
-----------------------------.(((((((((....)))))))))..(((((((((......))))))))).........................((((((....)))))). ( -25.40)
>consensus
_____________________________UUAAAGCGCUGAAUAGCACUUUGUCUGGAAAAUCAGUCUGGGUUUUCCAUUAACCCAUAUAUUCAUAAUUAAUUGUUUGCCUGAGCAGACU
..............................(((((.(((....))).)))))..(((((((((......))))))))).........................((((((....)))))). (-20.52 = -20.72 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:27 2006