Locus 10172

Sequence ID	3R_DroMel_CAF1
Location	27,300,370 – 27,300,614
Length	244
Max. P	0.938719

overview

Window 1

Location	27,300,370 – 27,300,481
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	93.83
Mean single sequence MFE	-32.08
Consensus MFE	-25.21
Energy contribution	-25.77
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-3.45
Structure conservation index	0.79
SVM decision value	1.21
SVM RNA-class probability	0.930646
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27300370 111 + 27905053
ACACGACUUUCAUGUUAGCAAGUCGUUC-GCUAACAGUAA-AAUCAAUAAGUACCAGGCGGCUUAUUAUGAGCCUUGCU-------AACAGUGAGCUAAAUAACUUGGCUCACAGAACAU
........(((.((((((((((..((((-((.....))..-....(((((((........)))))))..))))))))))-------))))(((((((((.....))))))))).)))... ( -34.70)
>DroSec_CAF1 5377 111 + 1
ACACGACUUUCAUGUUAGCAAGUCGUUC-GCUAACAGUAA-AAUCAAUAAGUACCAGGCGGCUUAUUAUGAGCCUUGCU-------AACAGUGAGCUAAAUAACUUGGCUCACAGAACAU
........(((.((((((((((..((((-((.....))..-....(((((((........)))))))..))))))))))-------))))(((((((((.....))))))))).)))... ( -34.70)
>DroSim_CAF1 5798 111 + 1
ACACGACUUUCAUGUUAGCAAGUCGUUC-GCUAACAGUAA-AAUCAAUAAGUACCAGGCGGCUUAUUAUGAGCCUUGCU-------AACAGUGAGCUAAAUAACUUGGCUCACAGAACAU
........(((.((((((((((..((((-((.....))..-....(((((((........)))))))..))))))))))-------))))(((((((((.....))))))))).)))... ( -34.70)
>DroEre_CAF1 5517 112 + 1
ACACGACUUUCAUGUUAGCAAGUCGUUC-UCUAACAGUAAAAAUCAAUAUGUACCAGGCGGCUUAUUAUGAGCCUUGCC-------AACAGUGAGCUAAAUAACUUGGCUCACAGAACAU
....(((((.(......).)))))((((-(..........................((((((((.....)))))..)))-------....(((((((((.....)))))))))))))).. ( -33.30)
>DroYak_CAF1 1509 119 + 1
ACACGACUUUCAUGUUAGCAAGUCGUUC-GCUAACAGUAAAAAUCAAUAAGUACCAGGCGGCUUAUUAUGAGCCUUGCUAACUGCUAACAGUGAGCUAAAUAACUUGGCUCACAGAACAU
........(((..(((((((((..((((-((.....)).......(((((((........)))))))..)))))))))))))........(((((((((.....))))))))).)))... ( -33.20)
>DroAna_CAF1 6050 112 + 1
ACACGACUUUCAUGUUAGCAAGUCGUUGUUGUAACAGUAAAAAUCAAUAAGUACCAGGCUGCCUAUUAUGAGCC-AGCG-------AACAGUGAACUAAAUAACUUGGCUCACAGAACAU
..(((((((.(......).)))))))((((.(..((((......(.....)......)))).......((((((-((..-------...((....)).......)))))))).).)))). ( -21.90)
>consensus
ACACGACUUUCAUGUUAGCAAGUCGUUC_GCUAACAGUAA_AAUCAAUAAGUACCAGGCGGCUUAUUAUGAGCCUUGCU_______AACAGUGAGCUAAAUAACUUGGCUCACAGAACAU
..(((((((.(......).))))))).................((...........((((((((.....)))))..)))...........(((((((((.....))))))))).)).... (-25.21 = -25.77 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	27,300,409 – 27,300,517
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	88.53
Mean single sequence MFE	-31.06
Consensus MFE	-25.64
Energy contribution	-26.78
Covariance contribution	1.14
Combinations/Pair	1.11
Mean z-score	-2.89
Structure conservation index	0.83
SVM decision value	1.29
SVM RNA-class probability	0.938719
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27300409 108 + 27905053
-AAUCAAUAAGUACCAGGCGGCUUAUUAUGAGCCUUGCU-------AACAGUGAGCUAAAUAACUUGGCUCACAGAACAUGCGGCAAUCAUCGUCGUU---CGCCUUUUGUACC-CCCUC
-.........((((.(((((((((.....))))).....-------....(((((((((.....))))))))).((((..((((......)))).)))---)))))...)))).-..... ( -34.10)
>DroSec_CAF1 5416 105 + 1
-AAUCAAUAAGUACCAGGCGGCUUAUUAUGAGCCUUGCU-------AACAGUGAGCUAAAUAACUUGGCUCACAGAACAUGCGGCAAUCAUCGUCGUU---CGCCUUUUGUACC-CC---
-.........((((.(((((((((.....))))).....-------....(((((((((.....))))))))).((((..((((......)))).)))---)))))...)))).-..--- ( -34.10)
>DroSim_CAF1 5837 105 + 1
-AAUCAAUAAGUACCAGGCGGCUUAUUAUGAGCCUUGCU-------AACAGUGAGCUAAAUAACUUGGCUCACAGAACAUGCGGCAAUCAUCGUCGUU---CGCCUUUUGUACC-CC---
-.........((((.(((((((((.....))))).....-------....(((((((((.....))))))))).((((..((((......)))).)))---)))))...)))).-..--- ( -34.10)
>DroEre_CAF1 5556 106 + 1
AAAUCAAUAUGUACCAGGCGGCUUAUUAUGAGCCUUGCC-------AACAGUGAGCUAAAUAACUUGGCUCACAGAACAUGCGGCAAUCAUCUUCGUU---CGCCUUUUGUACC-CC---
..........((((.(((((((((.....)))))(((((-------....(((((((((.....))))))))).(......))))))...........---.))))...)))).-..--- ( -33.90)
>DroYak_CAF1 1548 114 + 1
AAAUCAAUAAGUACCAGGCGGCUUAUUAUGAGCCUUGCUAACUGCUAACAGUGAGCUAAAUAACUUGGCUCACAGAACAUGCGCCAAUCAUCGUCGCU---CGCCUUCUGUUCCCCC---
...............(((((((((.....)))))..((.....)).....(((((((((.....))))))))).......(((.(.......).))).---.))))...........--- ( -28.00)
>DroAna_CAF1 6090 103 + 1
AAAUCAAUAAGUACCAGGCUGCCUAUUAUGAGCC-AGCG-------AACAGUGAACUAAAUAACUUGGCUCACAGAACAUGCAGCAAUCAUCGUUGAUGCUCGUCU-----CCC-CC---
..(((((..(.......(((((......((((((-((..-------...((....)).......))))))))........))))).....)..)))))........-----...-..--- ( -22.14)
>consensus
_AAUCAAUAAGUACCAGGCGGCUUAUUAUGAGCCUUGCU_______AACAGUGAGCUAAAUAACUUGGCUCACAGAACAUGCGGCAAUCAUCGUCGUU___CGCCUUUUGUACC_CC___
..........((((.(((((((((.....)))))................(((((((((.....))))))))).......(((((.......))))).....))))...))))....... (-25.64 = -26.78 +   1.14)

alignment

secondary structure

dotplot

Window 3

Location	27,300,447 – 27,300,557
Length	110
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.80
Mean single sequence MFE	-24.08
Consensus MFE	-16.31
Energy contribution	-16.65
Covariance contribution	0.34
Combinations/Pair	1.17
Mean z-score	-2.29
Structure conservation index	0.68
SVM decision value	0.96
SVM RNA-class probability	0.889255
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27300447 110 + 27905053
------AACAGUGAGCUAAAUAACUUGGCUCACAGAACAUGCGGCAAUCAUCGUCGUU---CGCCUUUUGUACC-CCCUCCCUCUGCUCUACAAUAGUCCAUCCAAUAGGCAUUAAUUUU
------....(((((((((.....))))))))).((((..((((......)))).)))---)((((.(((....-............................))).))))......... ( -24.05)
>DroSec_CAF1 5454 106 + 1
------AACAGUGAGCUAAAUAACUUGGCUCACAGAACAUGCGGCAAUCAUCGUCGUU---CGCCUUUUGUACC-CC----CCCUGCUCUACAAUAGGCCAUCCAAUAGUCAUUAAUUUU
------....(((((((((.....))))))))).((((..((((......)))).)))---)((((.(((((..-..----........))))).))))..................... ( -26.90)
>DroSim_CAF1 5875 106 + 1
------AACAGUGAGCUAAAUAACUUGGCUCACAGAACAUGCGGCAAUCAUCGUCGUU---CGCCUUUUGUACC-CC----CUCUGCUCUACAAUAGGCCAUCCAAUAGGCAUUAAUUUU
------....(((((((((.....))))))))).((((..((((......)))).)))---)((((.(((....-.(----((.(........).))).....))).))))......... ( -27.80)
>DroEre_CAF1 5595 96 + 1
------AACAGUGAGCUAAAUAACUUGGCUCACAGAACAUGCGGCAAUCAUCUUCGUU---CGCCUUUUGUACC-CC----CUCUG----------AGCAGUCGAAUAGGCAUUAAUUUU
------....(((((((((.....))))))))).((((.................)))---)((((((((.((.-.(----.....----------.)..)))))).))))......... ( -21.73)
>DroYak_CAF1 1588 103 + 1
ACUGCUAACAGUGAGCUAAAUAACUUGGCUCACAGAACAUGCGCCAAUCAUCGUCGCU---CGCCUUCUGUUCCCCC----CACUG----------AACAGUCCAAUAGGCAUUAAUUUU
..........(((((((((.....))))))))).......(((.(.......).))).---.((((.((((((....----....)----------)))))......))))......... ( -26.90)
>DroAna_CAF1 6128 93 + 1
------AACAGUGAACUAAAUAACUUGGCUCACAGAACAUGCAGCAAUCAUCGUUGAUGCUCGUCU-----CCC-CC----UUCU-----------AACAAGCCAUUAGGCAUUAAUUUU
------....((((.((((.....)))).)))).....(((.((((.(((....))))))))))..-----...-..----....-----------.....(((....)))......... ( -17.10)
>consensus
______AACAGUGAGCUAAAUAACUUGGCUCACAGAACAUGCGGCAAUCAUCGUCGUU___CGCCUUUUGUACC_CC____CUCUG__________AGCAAUCCAAUAGGCAUUAAUUUU
..........(((((((((.....))))))))).......(((((.......))))).....((((.........................................))))......... (-16.31 = -16.65 +   0.34)

alignment

secondary structure

dotplot

Window 4

Location	27,300,517 – 27,300,614
Length	97
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	80.99
Mean single sequence MFE	-16.75
Consensus MFE	-8.98
Energy contribution	-9.60
Covariance contribution	0.62
Combinations/Pair	1.05
Mean z-score	-2.26
Structure conservation index	0.54
SVM decision value	0.16
SVM RNA-class probability	0.611494
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27300517 97 + 27905053
CCUCUGCUCUACAAUAGUCCAUCCAAUAGGCAUUAAUUUUAGCCAUAUGCACUGGACUAUUCCAUACACUAUACACCA--------------UAUAGCAUACACCAGGGA----C
.(((((......(((((((((....((((((..........))).)))....))))))))).......(((((.....--------------))))).......))))).----. ( -21.60)
>DroSec_CAF1 5521 110 + 1
-CCCUGCUCUACAAUAGGCCAUCCAAUAGUCAUUAAUUUUAGCCAUAUGCACUGGACUAUUCCAUACACCAUACACCAUACACCAUAUAGCAUAUAGCAUACACCAGGGA----C
-(((((..........(((.........)))..........((.((((((..((((....)))).............(((.....))).)))))).))......))))).----. ( -19.00)
>DroSim_CAF1 5942 96 + 1
-CUCUGCUCUACAAUAGGCCAUCCAAUAGGCAUUAAUUUUAGCCAUAUGCACUGGACUAUUCCAUACACCAUACACCA--------------UAUAGCAUACACCAGGGA----C
-(((((...........(((........)))..........((.(((((...((((....))))............))--------------))).))......))))).----. ( -14.86)
>DroYak_CAF1 1662 97 + 1
-CACUG----------AACAGUCCAAUAGGCAUUAAUUUUAGCCAUAUGCACUAGACUAUUCCAUACACCAUACACCAUACAAC-------AUAUAGCAUACACCAGGGACCGAC
-.....----------..(.((((....(((..........))).(((((..................................-------.....)))))......)))).).. ( -11.53)
>consensus
_CUCUGCUCUACAAUAGGCCAUCCAAUAGGCAUUAAUUUUAGCCAUAUGCACUGGACUAUUCCAUACACCAUACACCA______________UAUAGCAUACACCAGGGA____C
.(((((......................(((..........))).(((((..((((....))))((.....)).......................)))))...)))))...... ( -8.98 =  -9.60 +   0.62)

alignment

secondary structure

dotplot

Window 5

Location	27,300,517 – 27,300,614
Length	97
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	80.99
Mean single sequence MFE	-28.72
Consensus MFE	-16.84
Energy contribution	-17.03
Covariance contribution	0.19
Combinations/Pair	1.12
Mean z-score	-2.20
Structure conservation index	0.59
SVM decision value	0.60
SVM RNA-class probability	0.794941
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27300517 97 - 27905053
G----UCCCUGGUGUAUGCUAUA--------------UGGUGUAUAGUGUAUGGAAUAGUCCAGUGCAUAUGGCUAAAAUUAAUGCCUAUUGGAUGGACUAUUGUAGAGCAGAGG
.----.(((((.(((((((((((--------------(...)))))))))))(.(((((((((.(.((...(((..........)))...)).)))))))))).)..).))).)) ( -29.30)
>DroSec_CAF1 5521 110 - 1
G----UCCCUGGUGUAUGCUAUAUGCUAUAUGGUGUAUGGUGUAUGGUGUAUGGAAUAGUCCAGUGCAUAUGGCUAAAAUUAAUGACUAUUGGAUGGCCUAUUGUAGAGCAGGG-
.----.(((((.(((((((((((((((((((...))))))))))))))))))(((....)))..((((...(((((.(((........)))...)))))...)))).).)))))- ( -34.90)
>DroSim_CAF1 5942 96 - 1
G----UCCCUGGUGUAUGCUAUA--------------UGGUGUAUGGUGUAUGGAAUAGUCCAGUGCAUAUGGCUAAAAUUAAUGCCUAUUGGAUGGCCUAUUGUAGAGCAGAG-
.----...(((.(((((((((((--------------(...)))))))))))((....((((((((.....(((..........)))))))))))..))........).)))..- ( -22.90)
>DroYak_CAF1 1662 97 - 1
GUCGGUCCCUGGUGUAUGCUAUAU-------GUUGUAUGGUGUAUGGUGUAUGGAAUAGUCUAGUGCAUAUGGCUAAAAUUAAUGCCUAUUGGACUGUU----------CAGUG-
.............((((((((((.-------.((....))..)))))))))).(((((((((((((.....(((..........)))))))))))))))----------)....- ( -27.80)
>consensus
G____UCCCUGGUGUAUGCUAUA______________UGGUGUAUGGUGUAUGGAAUAGUCCAGUGCAUAUGGCUAAAAUUAAUGCCUAUUGGAUGGCCUAUUGUAGAGCAGAG_
........(((..(((((((((((.................)))))))))))......((((((((.....(((..........)))))))))))..............)))... (-16.84 = -17.03 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:50:33 2006