Locus 6221

Sequence ID 3L_DroMel_CAF1
Location 16,533,282 – 16,533,456
Length 174
Max. P 0.911971
window9981 window9982 window9983

overview

Window 1

Location 16,533,282 – 16,533,396
Length 114
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 77.39
Mean single sequence MFE -32.25
Consensus MFE -16.31
Energy contribution -15.03
Covariance contribution -1.27
Combinations/Pair 1.45
Mean z-score -2.05
Structure conservation index 0.51
SVM decision value 0.55
SVM RNA-class probability 0.778328
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16533282 114 - 23771897
UAGGGGAGUGCCCGCCCAAGAGGGGGGGGGGUGCGGUGUCUCAGAUAGCAGAUCGUCUGAAAUAUCGGAAAAUAUCCAAAGUAUCUGUAGCGCUAGAAAAGUGCAAGCAAUCCG
....(((.(((((.(((....))).)).(((((((((((.((((((........)))))).)))))(((.....)))...))))))...(((((.....)))))..))).))). ( -42.00)
>DroSec_CAF1 146521 108 - 1
UAGGGGAGUGCCCGCCCAAAAGGGGACGGGG------GUCUCAGAUAGCAGAUCGUCUGAAAUAUCGGAAAAUAUCCAAAGUAUCUGUAGCGCUAGAAAAGUGCAAGCAAUCCG
..(((((((.(((((((.....))).)))).------).))).((((.(((.....)))...))))(((.....)))............(((((.....)))))......))). ( -33.60)
>DroSim_CAF1 149623 108 - 1
UAGGGGAGUGCCCGCCCAAAGGGGGACUUGG------GUCUCAGAUAGCAGAUCGUCUGAAAUAUCGGAAAAUAUCCAAAGUAUCUGUAGCGCUAGAAAAGUGCAAGCAAUCCG
....(((.(((..(((((..((....)))))------))..((((((.(((.....))).......(((.....)))....))))))..(((((.....)))))..))).))). ( -32.60)
>DroEre_CAF1 144335 99 - 1
UAGGGGAGUGCCC----AA-GGAG----GAG------GUCUCAGAUAGCAGAUCGUCUGAAAUAUCGGGAAAUAUCUGAAGUAUCUGUAGCGCUAGAGAAGUGCAACCAAUCCG
..(((.....)))----..-(((.----..(------((..((((((.(((((..(((((....)))))....)))))...))))))..(((((.....))))).)))..))). ( -30.90)
>DroYak_CAF1 147403 99 - 1
UAGGGGAGUGCCC----AA-GGAG----GGG------GUCUCAGAUAGCAGAUCGUCUGAAAUAUCGGGAAAUAUCUGAAGUAUCUGUAGCGCUAGAAAAGUGCAACCAAUCCG
..(((.....)))----..-(((.----.((------....((((((.(((((..(((((....)))))....)))))...))))))..(((((.....)))))..))..))). ( -32.70)
>DroAna_CAF1 147746 86 - 1
UAGGGGAGUGUCC----AA-GGAG----GCG------GAGGUGGAGAUGGGAUCGACUCAGAUCAUGACACACA-------------GAUCGCUGGAAAAGUGCAACCAAUCCC
...((((((.((.----..-.)).----))(------(..(((.......((((......))))......))).-------------...((((.....))))...))..)))) ( -21.72)
>consensus
UAGGGGAGUGCCC____AA_GGAG____GGG______GUCUCAGAUAGCAGAUCGUCUGAAAUAUCGGAAAAUAUCCAAAGUAUCUGUAGCGCUAGAAAAGUGCAACCAAUCCG
..(((.....))).......(((.................((.((((.(((.....)))...)))).))....................(((((.....)))))......))). (-16.31 = -15.03 +  -1.27)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 16,533,322 – 16,533,421
Length 99
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 80.62
Mean single sequence MFE -25.75
Consensus MFE -18.54
Energy contribution -17.18
Covariance contribution -1.36
Combinations/Pair 1.44
Mean z-score -2.27
Structure conservation index 0.72
SVM decision value 1.08
SVM RNA-class probability 0.911971
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16533322 99 - 23771897
AACAAAGGAGGGGCAUUCAAUUGAUUAGGGGAGUGCCCGCCCAAGAGGGGGGGGGGUGCGGUGUCUCAGAUAGCAGAUCGUCUGAAAUAUCGGAAAAUA
.........(((((((((....))........(..(((.(((.......))).)))..).))))))).((((.(((.....)))...))))........ ( -30.70)
>DroSec_CAF1 146561 93 - 1
AACAAAGGAGGGGCAUUCAAUUGAUUAGGGGAGUGCCCGCCCAAAAGGGGACGGGG------GUCUCAGAUAGCAGAUCGUCUGAAAUAUCGGAAAAUA
.......(((((((((((..(......)..))))))))((((....(....)..))------))))).((((.(((.....)))...))))........ ( -30.80)
>DroSim_CAF1 149663 93 - 1
AACAAAGGAGGGGCAUUCAAUUGAUUAGGGGAGUGCCCGCCCAAAGGGGGACUUGG------GUCUCAGAUAGCAGAUCGUCUGAAAUAUCGGAAAAUA
.......(((((((((((..(......)..))))))))(((((..((....)))))------))))).((((.(((.....)))...))))........ ( -32.00)
>DroEre_CAF1 144375 84 - 1
AACAAAGGAGGGGCAUUCAAUUGAUUAGGGGAGUGCCC----AA-GGAG----GAG------GUCUCAGAUAGCAGAUCGUCUGAAAUAUCGGGAAAUA
..........((((((((..(......)..))))))))----..-....----...------.((((.((((.(((.....)))...)))))))).... ( -23.00)
>DroYak_CAF1 147443 84 - 1
CACAAAGGAGGGGCAUUCAAUUGAUUAGGGGAGUGCCC----AA-GGAG----GGG------GUCUCAGAUAGCAGAUCGUCUGAAAUAUCGGGAAAUA
..........((((((((..(......)..))))))))----..-....----...------.((((.((((.(((.....)))...)))))))).... ( -23.00)
>DroAna_CAF1 147773 84 - 1
AACAAAGGCGGCGCAUUCAAUUGAUUAGGGGAGUGUCC----AA-GGAG----GCG------GAGGUGGAGAUGGGAUCGACUCAGAUCAUGACACACA
.........((.((((((..(......)..))))))))----..-....----...------...(((.......((((......))))......))). ( -15.02)
>consensus
AACAAAGGAGGGGCAUUCAAUUGAUUAGGGGAGUGCCC____AA_GGAG____GGG______GUCUCAGAUAGCAGAUCGUCUGAAAUAUCGGAAAAUA
..........((((((((..(......)..))))))))...........................((.((((.(((.....)))...)))).))..... (-18.54 = -17.18 +  -1.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 16,533,362 – 16,533,456
Length 94
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 78.53
Mean single sequence MFE -24.38
Consensus MFE -11.74
Energy contribution -11.30
Covariance contribution -0.44
Combinations/Pair 1.23
Mean z-score -2.06
Structure conservation index 0.48
SVM decision value 0.52
SVM RNA-class probability 0.765975
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16533362 94 - 23771897
-AAUGCCGAUGGGAAUGGGAAUGGG---UUGAAAAUGCAAACAAAGGAGGGGCAUUCAAUUGAUUAGGGGAGUGCCCGCCCAAGAGGGGGGGGGGUGC
-....((.((....)).))(((.((---((((..((((...(......)..)))))))))).)))......(..(((.(((.......))).)))..) ( -27.10)
>DroSec_CAF1 146598 91 - 1
-AAUGCCGAUGCGAAUGGGAAUGGG---UUGAAAAUGCAAACAAAGGAGGGGCAUUCAAUUGAUUAGGGGAGUGCCCGCCCAAAAGGGGACGGGG---
-....(((.(.(...((((..((..---(((......))).))......((((((((..(......)..)))))))).))))...).)..)))..--- ( -24.20)
>DroSim_CAF1 149700 91 - 1
-AAUGCCGAUGCGAAUGGGAAUGGG---UUGAAAAUGCAAACAAAGGAGGGGCAUUCAAUUGAUUAGGGGAGUGCCCGCCCAAAGGGGGACUUGG---
-....((.((....)).))..((((---(((......))..........((((((((..(......)..))))))))))))).(((....)))..--- ( -24.70)
>DroYak_CAF1 147480 80 - 1
-AAUGCCGAUGCGAU--GGCAUGGG---UUGCAAAUGCACACAAAGGAGGGGCAUUCAAUUGAUUAGGGGAGUGCCC----AA-GGAG----GGG---
-...(((.((((...--.)))).))---)(((....)))..........((((((((..(......)..))))))))----..-....----...--- ( -24.70)
>DroAna_CAF1 147810 79 - 1
AAAUGCCUUUGG-------AGGGGGCUUUGGAGAAUGCAAACAAAGGCGGCGCAUUCAAUUGAUUAGGGGAGUGUCC----AA-GGAG----GCG---
....((((((..-------....(.(((((...........))))).)((.((((((..(......)..))))))))----..-))))----)).--- ( -21.20)
>consensus
_AAUGCCGAUGCGAAUGGGAAUGGG___UUGAAAAUGCAAACAAAGGAGGGGCAUUCAAUUGAUUAGGGGAGUGCCCGCCCAA_GGGGG___GGG___
.....((.((..........)).))........................((((((((..(......)..))))))))..................... (-11.74 = -11.30 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:04 2006