Locus 5840

Sequence ID	2R_DroMel_CAF1
Location	18,495,017 – 18,495,355
Length	338
Max. P	0.999928

overview

Window 2

Location	18,495,017 – 18,495,128
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.80
Mean single sequence MFE	-25.52
Consensus MFE	-19.49
Energy contribution	-20.13
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.49
Structure conservation index	0.76
SVM decision value	-0.05
SVM RNA-class probability	0.505682
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18495017 111 + 20766785
CUAAGCAAGGCCACUUUUCAAAUGACCUCAAUUGGUU---------UUUUUUGCUGGCCUAAUGAAUAUUUCAGUUUUGGCAACAUCGCUAACGCCAUAGACGUCCAUCGAUGGCCAUUU
.......((((((.....((((.((((......))))---------...)))).))))))((((........(((..((....))..)))...(((((.((......)).))))))))). ( -27.10)
>DroSec_CAF1 13640 111 + 1
CUAAGCAAGGCCAAUUUUCAAAUGACCUCAAUUGGUU---------UUUUUUGCUGGCCUAAUGAAUAUUUCAGUUUUGGCAACAUCGCUAACGCCAUAGACGUCCAUCGAUGGCCAUUU
.......((((((.....((((.((((......))))---------...)))).))))))((((........(((..((....))..)))...(((((.((......)).))))))))). ( -27.10)
>DroSim_CAF1 2307 116 + 1
CUAAGCAAGGCCAAUUUUCAAAUGACCUCAAUUGGUUUUGUU----UUUUUUGCUGGCCUAAUGAAUAUUUCAGUUUUGGCAACAUCGCUAACGCCAUAGACGUCCAUCGAUGGCCAUUU
..((((((((((((((.((....))....)))))))))))))----).......(((((...(((.....)))((((((((............)))).))))..........)))))... ( -28.00)
>DroEre_CAF1 19127 119 + 1
CUAAGCAAGUC-AACGUUUAAAUGACCUCAAUAGGUUUUCUUUUUUUUUUUUGCUGGCCUAAUGAAUAUUUCAGUUUUGGCAACAUCGCUAACGCCAUAGACGUCCAUCGAUGGCCAUAU
...((((((..-...........(((((....)))))............))))))((((...(((.....)))((((((((............)))).))))..........)))).... ( -23.71)
>DroYak_CAF1 20923 93 + 1
CUAAGCAAGUC-AG------------CUCAAUAGGUUU--------UUUUUUGCUGGCCUAAUGAAUAUUUCAGUUUUGGCAACAUCG------CCAUGGACGUCUAUCGAUGGCCAUUU
...((((((..-((------------((.....)))).--------...))))))((((..............((((((((......)------))).))))(((....))))))).... ( -21.70)
>consensus
CUAAGCAAGGCCAAUUUUCAAAUGACCUCAAUUGGUUU________UUUUUUGCUGGCCUAAUGAAUAUUUCAGUUUUGGCAACAUCGCUAACGCCAUAGACGUCCAUCGAUGGCCAUUU
...((((((..............((((......))))............))))))((((...(((.....)))((((((((............)))).))))..........)))).... (-19.49 = -20.13 +   0.64)

alignment

secondary structure

dotplot

Window 3

Location	18,495,017 – 18,495,128
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.80
Mean single sequence MFE	-27.28
Consensus MFE	-20.01
Energy contribution	-21.86
Covariance contribution	1.85
Combinations/Pair	1.00
Mean z-score	-1.68
Structure conservation index	0.73
SVM decision value	0.16
SVM RNA-class probability	0.612823
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18495017 111 - 20766785
AAAUGGCCAUCGAUGGACGUCUAUGGCGUUAGCGAUGUUGCCAAAACUGAAAUAUUCAUUAGGCCAGCAAAAAA---------AACCAAUUGAGGUCAUUUGAAAAGUGGCCUUGCUUAG
...(((((((((...(((((.....)))))..))))(((.....)))..............)))))........---------........(((((((((.....)))))))))...... ( -30.10)
>DroSec_CAF1 13640 111 - 1
AAAUGGCCAUCGAUGGACGUCUAUGGCGUUAGCGAUGUUGCCAAAACUGAAAUAUUCAUUAGGCCAGCAAAAAA---------AACCAAUUGAGGUCAUUUGAAAAUUGGCCUUGCUUAG
...(((((((((...(((((.....)))))..)))))..)))).................(((((((...(((.---------.(((......)))..))).....)))))))....... ( -30.40)
>DroSim_CAF1 2307 116 - 1
AAAUGGCCAUCGAUGGACGUCUAUGGCGUUAGCGAUGUUGCCAAAACUGAAAUAUUCAUUAGGCCAGCAAAAAA----AACAAAACCAAUUGAGGUCAUUUGAAAAUUGGCCUUGCUUAG
...(((((((((...(((((.....)))))..))))(((.....)))..............)))))((((....----..(((......))).(((((.........))))))))).... ( -28.80)
>DroEre_CAF1 19127 119 - 1
AUAUGGCCAUCGAUGGACGUCUAUGGCGUUAGCGAUGUUGCCAAAACUGAAAUAUUCAUUAGGCCAGCAAAAAAAAAAAAGAAAACCUAUUGAGGUCAUUUAAACGUU-GACUUGCUUAG
.....(((((.(((....))).)))))(((((((.(((((((.((..(((.....))))).)).)))))..........(((..((((....))))..)))...))))-)))........ ( -27.10)
>DroYak_CAF1 20923 93 - 1
AAAUGGCCAUCGAUAGACGUCCAUGG------CGAUGUUGCCAAAACUGAAAUAUUCAUUAGGCCAGCAAAAAA--------AAACCUAUUGAG------------CU-GACUUGCUUAG
...(((((...(((....)))..(((------((....)))))..................)))))........--------........((((------------(.-.....))))). ( -20.00)
>consensus
AAAUGGCCAUCGAUGGACGUCUAUGGCGUUAGCGAUGUUGCCAAAACUGAAAUAUUCAUUAGGCCAGCAAAAAA________AAACCAAUUGAGGUCAUUUGAAAAUUGGCCUUGCUUAG
...(((((((((...(((((.....)))))..))))(((.....)))..............))))).........................(((((((.........)))))))...... (-20.01 = -21.86 +   1.85)

alignment

secondary structure

dotplot

Window 4

Location	18,495,054 – 18,495,168
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.16
Mean single sequence MFE	-24.46
Consensus MFE	-20.60
Energy contribution	-21.04
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.66
Structure conservation index	0.84
SVM decision value	1.06
SVM RNA-class probability	0.908809
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18495054 114 + 20766785
------UUUUUUGCUGGCCUAAUGAAUAUUUCAGUUUUGGCAACAUCGCUAACGCCAUAGACGUCCAUCGAUGGCCAUUUCCAGCUCGAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUU
------......(((((...((((........(((..((....))..)))...(((((.((......)).))))))))).)))))........((((...............)))).... ( -24.26)
>DroSec_CAF1 13677 114 + 1
------UUUUUUGCUGGCCUAAUGAAUAUUUCAGUUUUGGCAACAUCGCUAACGCCAUAGACGUCCAUCGAUGGCCAUUUCCAGCUCGAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUU
------......(((((...((((........(((..((....))..)))...(((((.((......)).))))))))).)))))........((((...............)))).... ( -24.26)
>DroSim_CAF1 2347 116 + 1
UU----UUUUUUGCUGGCCUAAUGAAUAUUUCAGUUUUGGCAACAUCGCUAACGCCAUAGACGUCCAUCGAUGGCCAUUUCCAGCUCUAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUU
..----......(((((...((((........(((..((....))..)))...(((((.((......)).))))))))).)))))........((((...............)))).... ( -24.26)
>DroEre_CAF1 19166 120 + 1
UUUUUUUUUUUUGCUGGCCUAAUGAAUAUUUCAGUUUUGGCAACAUCGCUAACGCCAUAGACGUCCAUCGAUGGCCAUAUCCAGCUGGAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUU
............(((((((...(((.....))).....)))......((....))..............(((((.......((((((....)))))).....))))).....)))).... ( -28.30)
>DroYak_CAF1 20948 108 + 1
------UUUUUUGCUGGCCUAAUGAAUAUUUCAGUUUUGGCAACAUCG------CCAUGGACGUCUAUCGAUGGCCAUUUCCCACUCGAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUU
------......(((((................((((((((......)------))).))))....((((((((.......))).))))))))))......................... ( -21.20)
>consensus
______UUUUUUGCUGGCCUAAUGAAUAUUUCAGUUUUGGCAACAUCGCUAACGCCAUAGACGUCCAUCGAUGGCCAUUUCCAGCUCGAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUU
............(((((................((((((((............)))).)))).......(((((.......(((((......))))).....)))))....))))).... (-20.60 = -21.04 +   0.44)

alignment

secondary structure

dotplot

Window 5

Location	18,495,054 – 18,495,168
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.16
Mean single sequence MFE	-34.72
Consensus MFE	-31.58
Energy contribution	-32.42
Covariance contribution	0.84
Combinations/Pair	1.03
Mean z-score	-2.88
Structure conservation index	0.91
SVM decision value	4.61
SVM RNA-class probability	0.999928
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18495054 114 - 20766785
AAAGGCUGAUUGAGAUGGAGGAGCAGCUGGAUCGAGCUGGAAAUGGCCAUCGAUGGACGUCUAUGGCGUUAGCGAUGUUGCCAAAACUGAAAUAUUCAUUAGGCCAGCAAAAAA------
...((((...((((((...((..(((((......)))))....(((((((((...(((((.....)))))..)))))..))))...))...)).))))...)))).........------ ( -35.50)
>DroSec_CAF1 13677 114 - 1
AAAGGCUGAUUGAGAUGGAGGAGCAGCUGGAUCGAGCUGGAAAUGGCCAUCGAUGGACGUCUAUGGCGUUAGCGAUGUUGCCAAAACUGAAAUAUUCAUUAGGCCAGCAAAAAA------
...((((...((((((...((..(((((......)))))....(((((((((...(((((.....)))))..)))))..))))...))...)).))))...)))).........------ ( -35.50)
>DroSim_CAF1 2347 116 - 1
AAAGGCUGAUUGAGAUGGAGGAGCAGCUGGAUAGAGCUGGAAAUGGCCAUCGAUGGACGUCUAUGGCGUUAGCGAUGUUGCCAAAACUGAAAUAUUCAUUAGGCCAGCAAAAAA----AA
...((((...((((((...((..(((((......)))))....(((((((((...(((((.....)))))..)))))..))))...))...)).))))...)))).........----.. ( -35.50)
>DroEre_CAF1 19166 120 - 1
AAAGGCUGAUUGAGAUGGAGGAGCAGCUGGAUCCAGCUGGAUAUGGCCAUCGAUGGACGUCUAUGGCGUUAGCGAUGUUGCCAAAACUGAAAUAUUCAUUAGGCCAGCAAAAAAAAAAAA
...((((...((((((...((..((((((....))))))....(((((((((...(((((.....)))))..)))))..))))...))...)).))))...))))............... ( -39.60)
>DroYak_CAF1 20948 108 - 1
AAAGGCUGAUUGAGAUGGAGGAGCAGCUGGAUCGAGUGGGAAAUGGCCAUCGAUAGACGUCCAUGG------CGAUGUUGCCAAAACUGAAAUAUUCAUUAGGCCAGCAAAAAA------
...((((((((.((.((......)).)).)))).(((.((..((.(((((.(((....))).))))------).))....))...))).............)))).........------ ( -27.50)
>consensus
AAAGGCUGAUUGAGAUGGAGGAGCAGCUGGAUCGAGCUGGAAAUGGCCAUCGAUGGACGUCUAUGGCGUUAGCGAUGUUGCCAAAACUGAAAUAUUCAUUAGGCCAGCAAAAAA______
...((((...((((((...((..(((((......)))))....(((((((((...(((((.....)))))..)))))..))))...))...)).))))...))))............... (-31.58 = -32.42 +   0.84)

alignment

secondary structure

dotplot

Window 6

Location	18,495,088 – 18,495,208
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-23.15
Consensus MFE	-18.62
Energy contribution	-19.26
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.81
Structure conservation index	0.80
SVM decision value	0.65
SVM RNA-class probability	0.812413
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18495088 120 + 20766785
CAACAUCGCUAACGCCAUAGACGUCCAUCGAUGGCCAUUUCCAGCUCGAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUUGGCUCAUACAUAACCCAGUAAAUCCUUUUCCAGCUCGAUG
...(((((((...((((.((.(.......(((((.......(((((......))))).....))))).......).)).))))...(((........)))...........)))..)))) ( -23.04)
>DroSec_CAF1 13711 120 + 1
CAACAUCGCUAACGCCAUAGACGUCCAUCGAUGGCCAUUUCCAGCUCGAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUUGGCUCAUACAUAACCCAGUAAAUCCUUUUCCAGCUCGAUG
...(((((((...((((.((.(.......(((((.......(((((......))))).....))))).......).)).))))...(((........)))...........)))..)))) ( -23.04)
>DroSim_CAF1 2383 120 + 1
CAACAUCGCUAACGCCAUAGACGUCCAUCGAUGGCCAUUUCCAGCUCUAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUUGGCUCAUACAUAACCCAGUAAAUCCUUUUCCAGCUCGAUG
...(((((((...((((.((.(.......(((((.......(((((......))))).....))))).......).)).))))...(((........)))...........)))..)))) ( -23.04)
>DroEre_CAF1 19206 120 + 1
CAACAUCGCUAACGCCAUAGACGUCCAUCGAUGGCCAUAUCCAGCUGGAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUUGGCUCAUACAUAACCCAGUAAAUCCUUUUCCAGCUCGAUG
...(((((((...((((.((.(.......(((((.......((((((....)))))).....))))).......).)).))))...(((........)))...........)))..)))) ( -27.74)
>DroYak_CAF1 20982 114 + 1
CAACAUCG------CCAUGGACGUCUAUCGAUGGCCAUUUCCCACUCGAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUUGGCUCAUACAUAACCCGGUAAAUCCUUUUCCAGCUCUAUG
........------.((((((.....((((((((.......))).)))))...((((................((((...))))............((.....)).....)))))))))) ( -18.90)
>consensus
CAACAUCGCUAACGCCAUAGACGUCCAUCGAUGGCCAUUUCCAGCUCGAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUUGGCUCAUACAUAACCCAGUAAAUCCUUUUCCAGCUCGAUG
...(((((.....((((.((.(.......(((((.......(((((......))))).....))))).......).)).))))...(((........)))...............))))) (-18.62 = -19.26 +   0.64)

alignment

secondary structure

dotplot

Window 7

Location	18,495,128 – 18,495,248
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.00
Mean single sequence MFE	-21.62
Consensus MFE	-18.40
Energy contribution	-18.80
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.29
Structure conservation index	0.85
SVM decision value	1.70
SVM RNA-class probability	0.972652
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18495128 120 + 20766785
CCAGCUCGAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUUGGCUCAUACAUAACCCAGUAAAUCCUUUUCCAGCUCGAUGGCAUCGUUGCCAAUUUUCACACCAGCGACAAUUACUCAAA
...(((.((((.(((((................((((...))))..(((........)))..........))))).)))((((....))))..........).))).............. ( -21.10)
>DroSec_CAF1 13751 120 + 1
CCAGCUCGAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUUGGCUCAUACAUAACCCAGUAAAUCCUUUUCCAGCUCGAUGGCAUCGUUGCCAAUUUUCACACCAGCGACAAUUACUCAAA
...(((.((((.(((((................((((...))))..(((........)))..........))))).)))((((....))))..........).))).............. ( -21.10)
>DroSim_CAF1 2423 120 + 1
CCAGCUCUAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUUGGCUCAUACAUAACCCAGUAAAUCCUUUUCCAGCUCGAUGGCAUCGUUGCCAAUUUUCACACCAGCGACAAUUACUCAAA
...(((..(((.(((((................((((...))))..(((........)))..........))))).)))((((....))))............))).............. ( -20.30)
>DroEre_CAF1 19246 120 + 1
CCAGCUGGAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUUGGCUCAUACAUAACCCAGUAAAUCCUUUUCCAGCUCGAUGGCAUCGUUGCCAAUUUUCACACCAGCGACAAUUACUCAAA
...((((((((.(((((................((((...))))..(((........)))..........))))).)))((((....))))..........))))).............. ( -27.60)
>DroYak_CAF1 21016 120 + 1
CCCACUCGAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUUGGCUCAUACAUAACCCGGUAAAUCCUUUUCCAGCUCUAUGGCAUCGUUGCCAAUUUUCACACCAGCGACAAUUACUCAAA
.....(((....(((((................((((...))))............((.....)).....)))))...(((((....))))).............)))............ ( -18.00)
>consensus
CCAGCUCGAUCCAGCUGCUCCUCCAUCUCAAUCAGCCUUUGGCUCAUACAUAACCCAGUAAAUCCUUUUCCAGCUCGAUGGCAUCGUUGCCAAUUUUCACACCAGCGACAAUUACUCAAA
...(((..(((.(((((................((((...))))..(((........)))..........))))).)))((((....))))............))).............. (-18.40 = -18.80 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	18,495,248 – 18,495,355
Length	107
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	79.59
Mean single sequence MFE	-35.02
Consensus MFE	-22.38
Energy contribution	-24.75
Covariance contribution	2.37
Combinations/Pair	1.06
Mean z-score	-2.19
Structure conservation index	0.64
SVM decision value	1.19
SVM RNA-class probability	0.928372
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18495248 107 - 20766785
GAGCUGUGACUGCGGGGGCGGG-------CGGGAAAAGUCCGGGAAAAGCGGGUCAGGGAAAAGGGAGCGAGGACGAGGACAGUGGUAACCCAUGUUUUUGUUGUUGCCAACGG
...((.(((((((.....((((-------(.......)))))......)).))))).))......(.((((.((((((((((.(((....))))))))))))).)))))..... ( -36.30)
>DroSec_CAF1 13871 114 - 1
GAGCUGUGACUGCGGGGGCGGGAAAAGUCCGGGAAAAGUCCGGGAAAAGCGGGUCAGAGAGAAGGAAGCGAGGACGAGGACAGUGGUGACCCAUGUUCUUGUUGUUGCCAACGG
((.((((..((((....))))......(((.(((....))).)))...)))).))............((((.((((((((((.(((....))))))))))))).))))...... ( -40.70)
>DroSim_CAF1 2543 92 - 1
GAGCUGUGACUGCGGGGGCGGGA----------------------AAAGCGGGUCAGGGAGAAGGGAGCGAGGACGAGGACAGUGGUGACCCAUGUUUUUGUUGUUGCCAACGG
((.((((..((((....))))..----------------------...)))).))..........(.((((.((((((((((.(((....))))))))))))).)))))..... ( -30.50)
>DroEre_CAF1 19366 105 - 1
GAGCUCUGACUGCGGGGGCGGGA-UGGACUGGUAAAAGUCCUGGAAAAGCGGGUCAGGGAAAAGGGGGAG----UGAGGACAG----GAGCCAUGUUUUUGUUGUUGCCAACGG
...((((((((((.....(((((-(............)))))).....)).)))))))).....(..(.(----..(.(((((----((((...))))))))).)..))..).. ( -32.60)
>consensus
GAGCUGUGACUGCGGGGGCGGGA______CGGGAAAAGUCCGGGAAAAGCGGGUCAGGGAAAAGGGAGCGAGGACGAGGACAGUGGUGACCCAUGUUUUUGUUGUUGCCAACGG
((.((((..((((....)))).......((((.......)))).....)))).))........(...((((.((((((((((.(((....))))))))))))).))))...).. (-22.38 = -24.75 +   2.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:59 2006