Locus 5564

Sequence ID 3R_DroMel_CAF1
Location 14,715,089 – 14,715,227
Length 138
Max. P 0.999983
window9068 window9069 window9070 window9071

overview

Window 8

Location 14,715,089 – 14,715,202
Length 113
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 94.42
Mean single sequence MFE -39.10
Consensus MFE -35.82
Energy contribution -36.62
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -3.79
Structure conservation index 0.92
SVM decision value 5.00
SVM RNA-class probability 0.999967
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14715089 113 + 27905053
GUUGGCCAACAAUUACAAGCCUCUGGGACAGAAAGCACUGCUGAUUGGGCUUCAAAGCCGUCACGUCGCCAACUAAUUAUCAACAUAAUUAAAAGGUGCCGUGACAAUCCCCG
...(((............)))...(((((((..(((...)))..)))((((....))))((((((.((((...(((((((....)))))))...)))).))))))..)))).. ( -33.60)
>DroSec_CAF1 133768 109 + 1
---GGCCAACAAUUACAGGCCUCUGGGGCAGAAAGCACUGCUGAUUGGGCUUCAAAGCCGUCACGUCGCCAACUAAUUAUCAACAUAAUUAAAAGGUGCCGUGACAAUCC-CG
---((((..........))))...(((((((......))))......((((....))))((((((.((((...(((((((....)))))))...)))).))))))...))-). ( -39.10)
>DroSim_CAF1 138713 110 + 1
---GGCCAACAAUUACAGGCCUUUGGGGCAGAAAGCACUGCUGAUUGGGCUUCAAAGCCGUCACGUCGCCAACUAAUUAUCAACAUAAUUAAAAGGUGCCGUGACAAUCCCCG
---((((..........))))...(((((((......)))).((((.((((....))))((((((.((((...(((((((....)))))))...)))).))))))))))))). ( -40.80)
>DroEre_CAF1 128873 110 + 1
---GGCCUAUAAUUAUAGGCCUCUGGGGCAGAAGGCACUGCUGAUUUGGCUUCAAAGCCGUCACGUCGCCAACUAAUUAUCAACAUAAUUAAAAGGUGCCGUGACAAUCCCCG
---(((((((....)))))))...(((((((......)))).((((.((((....))))((((((.((((...(((((((....)))))))...)))).))))))))))))). ( -44.60)
>DroYak_CAF1 135073 110 + 1
---GGCCAACAAUUACAGGCCUCUGGGGCAAAAAGGAGUGCUGAUUUGGCUUCAAAGCCGUCACGUCGCCAACUAAUUAUCAACAUAAUUAAAAGGUGCCGUGACAAUCCCCG
---((((..........))))...((((...................((((....))))((((((.((((...(((((((....)))))))...)))).))))))...)))). ( -37.40)
>consensus
___GGCCAACAAUUACAGGCCUCUGGGGCAGAAAGCACUGCUGAUUGGGCUUCAAAGCCGUCACGUCGCCAACUAAUUAUCAACAUAAUUAAAAGGUGCCGUGACAAUCCCCG
...((((..........))))...(((((((......)))).((((.((((....))))((((((.((((...(((((((....)))))))...)))).))))))))))))). (-35.82 = -36.62 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 14,715,089 – 14,715,202
Length 113
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 94.42
Mean single sequence MFE -40.42
Consensus MFE -38.70
Energy contribution -38.78
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -2.93
Structure conservation index 0.96
SVM decision value 5.32
SVM RNA-class probability 0.999983
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14715089 113 - 27905053
CGGGGAUUGUCACGGCACCUUUUAAUUAUGUUGAUAAUUAGUUGGCGACGUGACGGCUUUGAAGCCCAAUCAGCAGUGCUUUCUGUCCCAGAGGCUUGUAAUUGUUGGCCAAC
.(((((((((((((.(.((..((((((((....))))))))..)).).))))))((((....)))).)))).((((......)))))))...((((..........))))... ( -38.20)
>DroSec_CAF1 133768 109 - 1
CG-GGAUUGUCACGGCACCUUUUAAUUAUGUUGAUAAUUAGUUGGCGACGUGACGGCUUUGAAGCCCAAUCAGCAGUGCUUUCUGCCCCAGAGGCCUGUAAUUGUUGGCC---
.(-((...((((((.(.((..((((((((....))))))))..)).).))))))((((....))))......((((......)))))))...((((..........))))--- ( -38.50)
>DroSim_CAF1 138713 110 - 1
CGGGGAUUGUCACGGCACCUUUUAAUUAUGUUGAUAAUUAGUUGGCGACGUGACGGCUUUGAAGCCCAAUCAGCAGUGCUUUCUGCCCCAAAGGCCUGUAAUUGUUGGCC---
.(((((((((((((.(.((..((((((((....))))))))..)).).))))))((((....)))).)))).((((......)))))))...((((..........))))--- ( -41.10)
>DroEre_CAF1 128873 110 - 1
CGGGGAUUGUCACGGCACCUUUUAAUUAUGUUGAUAAUUAGUUGGCGACGUGACGGCUUUGAAGCCAAAUCAGCAGUGCCUUCUGCCCCAGAGGCCUAUAAUUAUAGGCC---
.(((((((((((((.(.((..((((((((....))))))))..)).).))))))((((....)))).)))).((((......)))))))...(((((((....)))))))--- ( -45.90)
>DroYak_CAF1 135073 110 - 1
CGGGGAUUGUCACGGCACCUUUUAAUUAUGUUGAUAAUUAGUUGGCGACGUGACGGCUUUGAAGCCAAAUCAGCACUCCUUUUUGCCCCAGAGGCCUGUAAUUGUUGGCC---
.(((((((((((((.(.((..((((((((....))))))))..)).).))))))((((....)))).)))).(((........))))))...((((..........))))--- ( -38.40)
>consensus
CGGGGAUUGUCACGGCACCUUUUAAUUAUGUUGAUAAUUAGUUGGCGACGUGACGGCUUUGAAGCCCAAUCAGCAGUGCUUUCUGCCCCAGAGGCCUGUAAUUGUUGGCC___
.(((((((((((((.(.((..((((((((....))))))))..)).).))))))((((....)))).)))).((((......)))))))...((((..........))))... (-38.70 = -38.78 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 14,715,123 – 14,715,227
Length 104
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 76.76
Mean single sequence MFE -26.47
Consensus MFE -13.86
Energy contribution -14.12
Covariance contribution 0.25
Combinations/Pair 1.10
Mean z-score -1.80
Structure conservation index 0.52
SVM decision value 0.25
SVM RNA-class probability 0.654514
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14715123 104 + 27905053
GCACUGCUGAUUGGGCUUCAAAGCCGUCACGUCGCCAACUAAUUAUCAACAUAAUUAAAAGGUGC-CGUGACAAUCCCCGGCGGGUCCUAGCCACUGACUGAUUA---
...((((((....((((....))))((((((.((((...(((((((....)))))))...)))).-))))))......))))))(((.........)))......--- ( -32.90)
>DroPse_CAF1 123589 89 + 1
----------UCACGCUUCAAAGCCGUCACGUCGCCAACUAAUUAUCAACAUAAUUAAAGGGUGC-CGUGACUGUACCGGGAGGGUC-----CCCUGACUGAUUA---
----------....(((....))).((((((.((((...(((((((....)))))))...)))).-)))))).....(((.(((...-----.)))..)))....--- ( -26.40)
>DroWil_CAF1 151076 87 + 1
--------------ACUUCAAAGCCAUCACGUCCUCAACUAAUUAUCAACAUAAUUAAAAGCUGC-CGUGACAUUUCCCGCAGGAA------CUGUGACUGAUUAUUA
--------------...........((((.(((..((..(((((((....)))))))....((((-.(.((....))).))))...------.)).)))))))..... ( -11.80)
>DroYak_CAF1 135104 104 + 1
GGAGUGCUGAUUUGGCUUCAAAGCCGUCACGUCGCCAACUAAUUAUCAACAUAAUUAAAAGGUGC-CGUGACAAUCCCCGGCGGGUCCGAACCACUGACUGAUUA---
(((.(((((....((((....))))((((((.((((...(((((((....)))))))...)))).-))))))......)))).).))).................--- ( -32.80)
>DroAna_CAF1 134192 97 + 1
---UGGGUGACUCAGCUUCAGAGCCGUCACGUCGCCAACUAAUUAUCAACAUAAUUAAAAGGUGCCCGUGGCAGUCCCCUGCGG-----CGCCACUGACUGAUUA---
---..(....)((((..((((.(((..((((.((((...(((((((....)))))))...))))..))))((((....))))))-----)....))))))))...--- ( -29.20)
>DroPer_CAF1 126023 89 + 1
----------UCACGCUUCAAAGCCGUCACGUCACCAACUAAUUAUCAACAUAAUUAAAAGGUGC-CGUGACUGUACCGGGAGGGUC-----CCCUGACUGAUUA---
----------....(((....))).((((((.((((...(((((((....)))))))...)))).-)))))).....(((.(((...-----.)))..)))....--- ( -25.70)
>consensus
__________UUACGCUUCAAAGCCGUCACGUCGCCAACUAAUUAUCAACAUAAUUAAAAGGUGC_CGUGACAGUCCCCGGAGGGUC_____CACUGACUGAUUA___
.................(((.....((((((..(((...(((((((....)))))))...)))...))))))....((....))...............)))...... (-13.86 = -14.12 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 14,715,123 – 14,715,227
Length 104
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 76.76
Mean single sequence MFE -29.47
Consensus MFE -18.29
Energy contribution -17.65
Covariance contribution -0.64
Combinations/Pair 1.17
Mean z-score -1.41
Structure conservation index 0.62
SVM decision value 0.24
SVM RNA-class probability 0.649736
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14715123 104 - 27905053
---UAAUCAGUCAGUGGCUAGGACCCGCCGGGGAUUGUCACG-GCACCUUUUAAUUAUGUUGAUAAUUAGUUGGCGACGUGACGGCUUUGAAGCCCAAUCAGCAGUGC
---.....((((..((((........))))..))))((((((-.(.((..((((((((....))))))))..)).).))))))((((....))))............. ( -31.60)
>DroPse_CAF1 123589 89 - 1
---UAAUCAGUCAGGG-----GACCCUCCCGGUACAGUCACG-GCACCCUUUAAUUAUGUUGAUAAUUAGUUGGCGACGUGACGGCUUUGAAGCGUGA----------
---.....((((.(((-----(....))))......((((((-.(.((..((((((((....))))))))..)).).))))))))))...........---------- ( -26.10)
>DroWil_CAF1 151076 87 - 1
UAAUAAUCAGUCACAG------UUCCUGCGGGAAAUGUCACG-GCAGCUUUUAAUUAUGUUGAUAAUUAGUUGAGGACGUGAUGGCUUUGAAGU--------------
........(((((((.------((((....)))).))(((((-.(..(..((((((((....))))))))..)..).)))))))))).......-------------- ( -20.00)
>DroYak_CAF1 135104 104 - 1
---UAAUCAGUCAGUGGUUCGGACCCGCCGGGGAUUGUCACG-GCACCUUUUAAUUAUGUUGAUAAUUAGUUGGCGACGUGACGGCUUUGAAGCCAAAUCAGCACUCC
---.........((((.(((((.....)))))((((((((((-.(.((..((((((((....))))))))..)).).))))))((((....)))).))))..)))).. ( -33.10)
>DroAna_CAF1 134192 97 - 1
---UAAUCAGUCAGUGGCG-----CCGCAGGGGACUGCCACGGGCACCUUUUAAUUAUGUUGAUAAUUAGUUGGCGACGUGACGGCUCUGAAGCUGAGUCACCCA---
---...(((((...(((.(-----((((((....))))((((..(.((..((((((((....))))))))..)).).))))..))).)))..)))))........--- ( -35.10)
>DroPer_CAF1 126023 89 - 1
---UAAUCAGUCAGGG-----GACCCUCCCGGUACAGUCACG-GCACCUUUUAAUUAUGUUGAUAAUUAGUUGGUGACGUGACGGCUUUGAAGCGUGA----------
---.....((((.(((-----(....))))......((((((-.((((..((((((((....))))))))..)))).))))))))))...........---------- ( -30.90)
>consensus
___UAAUCAGUCAGUG_____GACCCGCCGGGGACUGUCACG_GCACCUUUUAAUUAUGUUGAUAAUUAGUUGGCGACGUGACGGCUUUGAAGCCUAA__________
........((((.(((.........)))........((((((....((..((((((((....))))))))..))...))))))))))..................... (-18.29 = -17.65 +  -0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:12 2006