Locus 5589

Sequence ID	2R_DroMel_CAF1
Location	17,860,203 – 17,860,377
Length	174
Max. P	0.989457

overview

Window 7

Location	17,860,203 – 17,860,315
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.07
Mean single sequence MFE	-37.10
Consensus MFE	-27.18
Energy contribution	-27.26
Covariance contribution	0.08
Combinations/Pair	1.08
Mean z-score	-2.22
Structure conservation index	0.73
SVM decision value	0.95
SVM RNA-class probability	0.889044
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17860203 112 - 20766785
GCAAAGCUGAUUGCUGUCAGUUUUGCGGCCGAAGGAGGAGCAGCAUUCUACUGGCGAUG-UAGAUUGCAGCGAAAUCGCUUGGCAAA--GAACAGGGGCGGAGAUUGGU-----UUAUGU
(((((((..((..(((((.(((((...(((((..((...((.(((.(((((.......)-)))).))).))....))..)))))..)--))))...)))))..))..))-----)).))) ( -39.90)
>DroSec_CAF1 25587 110 - 1
GCAAAGCUGAUUGCUGUCAGUUUUGCGGCCGAAGGAGGA-CAGCAUUCUGCUGGCGAUG-UAGAUUGCAGCGAAAUCGUUUGGCAAA--CAACAGGGGCGGAGAU-GGU-----UUAUGU
(((((((((((....))))))))))).((((((.((...-((((.....))))(((((.-...))))).......)).))))))...--..(((..(((......-.))-----)..))) ( -38.60)
>DroSim_CAF1 26266 111 - 1
GCAAAGCUGAUUGCUGUCAGUUUUGCGGCCGAAGGAGGAGCAGCAUUCUGCUGGCGAUG-UAGAUUGCAGAGAAAUCGCUUGGCAAA--CAACAGGGGCGGAGAU-GGU-----UUAUGU
(((((((((((....))))))))))).(((.......((((.(((.(((((.......)-)))).))).((....)))))))))...--..(((..(((......-.))-----)..))) ( -37.21)
>DroEre_CAF1 28237 112 - 1
GCAAAGCUGAUUGCUGUCAGUUUUGCGGCCGAAGAAGGAGAA------UGCUGGCGAUG-UAGAUUGCAGCGAAAUCGCUUGGCAAACACAACAGGGGCGGAGAU-AGGGGGGCUUAUAA
(((((((((((....)))))))))))((((.......((...------(((((.((((.-...)))))))))...)).(((.((...(......)..)).)))..-.....))))..... ( -35.50)
>DroYak_CAF1 25926 108 - 1
GCAAAGCUGAUUGCUGUCAGUUUUGCGGCAAAAGGCGGAGAA------UGCUGGCGAUGGUAGAUUGCAGCGAAAUCGCUUGGCAAACACAACAGGAGCGGCGAU-GAUG-----CAUAA
(((((((((((....))))))))))).((...((((((....------(((((.((((.....)))))))))...)))))).)).............(((.....-..))-----).... ( -34.30)
>consensus
GCAAAGCUGAUUGCUGUCAGUUUUGCGGCCGAAGGAGGAGCAGCAUUCUGCUGGCGAUG_UAGAUUGCAGCGAAAUCGCUUGGCAAA__CAACAGGGGCGGAGAU_GGU_____UUAUGU
(((((((((((....))))))))))).(((((.....................(((((.....))))).(((....)))))))).................................... (-27.18 = -27.26 +   0.08)

alignment

secondary structure

dotplot

Window 8

Location	17,860,236 – 17,860,355
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.43
Mean single sequence MFE	-30.67
Consensus MFE	-24.16
Energy contribution	-25.22
Covariance contribution	1.06
Combinations/Pair	1.06
Mean z-score	-1.47
Structure conservation index	0.79
SVM decision value	-0.04
SVM RNA-class probability	0.511137
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17860236 119 + 20766785
AGCGAUUUCGCUGCAAUCUA-CAUCGCCAGUAGAAUGCUGCUCCUCCUUCGGCCGCAAAACUGACAGCAAUCAGCUUUGCUGUGGAUAAAGUUUUAUGCCGAGAAACUCAUUUAGUUUGC
...((((((((.(((.((((-(.......))))).))).)).......(((((...((((((.(((((((......)))))))......))))))..))))))))).))........... ( -34.60)
>DroSec_CAF1 25619 118 + 1
AACGAUUUCGCUGCAAUCUA-CAUCGCCAGCAGAAUGCUG-UCCUCCUUCGGCCGCAAAACUGACAGCAAUCAGCUUUGCUGUGGAUAAAGUUUUAUGCCGAGAAACUCAUUUAGUUUGC
............((((.(((-......((((.....))))-......((((((...((((((.(((((((......)))))))......))))))..)))))).........))).)))) ( -29.10)
>DroSim_CAF1 26298 119 + 1
AGCGAUUUCUCUGCAAUCUA-CAUCGCCAGCAGAAUGCUGCUCCUCCUUCGGCCGCAAAACUGACAGCAAUCAGCUUUGCUGUGGAUAAAGUUUUAUGCCGAGAAACUCAUUUAGUUUGC
...((((((((.((((((((-((..((((((((....)))))........))).(((((.((((......)))).)))))))))))).........))).)))))).))........... ( -33.20)
>DroEre_CAF1 28276 113 + 1
AGCGAUUUCGCUGCAAUCUA-CAUCGCCAGCA------UUCUCCUUCUUCGGCCGCAAAACUGACAGCAAUCAGCUUUGCUGUGGAUAAAGUUUUAUGCCGAGAAACUCAUUUAGUUUGC
((((....))))((((.(((-........(((------(....(((..((.((.(((((.((((......)))).))))).)).))..)))....)))).(((...)))...))).)))) ( -29.90)
>DroYak_CAF1 25960 114 + 1
AGCGAUUUCGCUGCAAUCUACCAUCGCCAGCA------UUCUCCGCCUUUUGCCGCAAAACUGACAGCAAUCAGCUUUGCUGUGGAUAAAGUUUUAUGCCGAGAAACUCAUUUAGUUUGC
((((....))))((((.(((.........(((------(.........((..(.(((((.((((......)))).))))).)..)).........)))).(((...)))...))).)))) ( -26.57)
>consensus
AGCGAUUUCGCUGCAAUCUA_CAUCGCCAGCAGAAUGCUGCUCCUCCUUCGGCCGCAAAACUGACAGCAAUCAGCUUUGCUGUGGAUAAAGUUUUAUGCCGAGAAACUCAUUUAGUUUGC
((((....))))((((.(((........(((((....))))).....((((((...((((((.(((((((......)))))))......))))))..)))))).........))).)))) (-24.16 = -25.22 +   1.06)

alignment

secondary structure

dotplot

Window 9

Location	17,860,236 – 17,860,355
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.43
Mean single sequence MFE	-38.86
Consensus MFE	-30.33
Energy contribution	-30.97
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-2.74
Structure conservation index	0.78
SVM decision value	1.78
SVM RNA-class probability	0.976965
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17860236 119 - 20766785
GCAAACUAAAUGAGUUUCUCGGCAUAAAACUUUAUCCACAGCAAAGCUGAUUGCUGUCAGUUUUGCGGCCGAAGGAGGAGCAGCAUUCUACUGGCGAUG-UAGAUUGCAGCGAAAUCGCU
.............(((((((((.((((....))))))...(((((((((((....)))))))))))........))))))).(((.(((((.......)-)))).)))((((....)))) ( -41.30)
>DroSec_CAF1 25619 118 - 1
GCAAACUAAAUGAGUUUCUCGGCAUAAAACUUUAUCCACAGCAAAGCUGAUUGCUGUCAGUUUUGCGGCCGAAGGAGGA-CAGCAUUCUGCUGGCGAUG-UAGAUUGCAGCGAAAUCGUU
((((.(((.....((((((((((((((....)))).....(((((((((((....))))))))))).)))).))))...-((((.....))))))....-))).))))((((....)))) ( -37.90)
>DroSim_CAF1 26298 119 - 1
GCAAACUAAAUGAGUUUCUCGGCAUAAAACUUUAUCCACAGCAAAGCUGAUUGCUGUCAGUUUUGCGGCCGAAGGAGGAGCAGCAUUCUGCUGGCGAUG-UAGAUUGCAGAGAAAUCGCU
((...........(((((((((.((((....))))))...(((((((((((....)))))))))))........))))))).(((.(((((.......)-)))).))).((....)))). ( -40.50)
>DroEre_CAF1 28276 113 - 1
GCAAACUAAAUGAGUUUCUCGGCAUAAAACUUUAUCCACAGCAAAGCUGAUUGCUGUCAGUUUUGCGGCCGAAGAAGGAGAA------UGCUGGCGAUG-UAGAUUGCAGCGAAAUCGCU
((((.(((.....(((.(.((((((....((((.((....(((((((((((....)))))))))))....)).))))....)------)))))).))).-))).))))((((....)))) ( -38.10)
>DroYak_CAF1 25960 114 - 1
GCAAACUAAAUGAGUUUCUCGGCAUAAAACUUUAUCCACAGCAAAGCUGAUUGCUGUCAGUUUUGCGGCAAAAGGCGGAGAA------UGCUGGCGAUGGUAGAUUGCAGCGAAAUCGCU
((((.(((.....(((.(.((((((.........(((...(((((((((((....))))))))))).((.....)))))..)------)))))).)))..))).))))((((....)))) ( -36.50)
>consensus
GCAAACUAAAUGAGUUUCUCGGCAUAAAACUUUAUCCACAGCAAAGCUGAUUGCUGUCAGUUUUGCGGCCGAAGGAGGAGCAGCAUUCUGCUGGCGAUG_UAGAUUGCAGCGAAAUCGCU
((((.(((.....(((.(.(((((..........(((...(((((((((((....)))))))))))...(....).))).........)))))).)))..))).))))((((....)))) (-30.33 = -30.97 +   0.64)

alignment

secondary structure

dotplot

Window 0

Location	17,860,275 – 17,860,377
Length	102
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	95.69
Mean single sequence MFE	-28.34
Consensus MFE	-25.90
Energy contribution	-26.50
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.78
Structure conservation index	0.91
SVM decision value	2.17
SVM RNA-class probability	0.989457
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17860275 102 - 20766785
UGCCGGCUGCCACUAAUUAAUUGCAAACUAAAUGAGUUUCUCGGCAUAAAACUUUAUCCACAGCAAAGCUGAUUGCUGUCAGUUUUGCGGCCGAAGGAGGAG
...((((((((...((((.(((........))).))))....))).................(((((((((((....))))))))))))))))......... ( -28.70)
>DroSec_CAF1 25658 101 - 1
UGCCGGCUGCCACUAAUUAAUUGCAAACUAAAUGAGUUUCUCGGCAUAAAACUUUAUCCACAGCAAAGCUGAUUGCUGUCAGUUUUGCGGCCGAAGGAGGA-
...((((((((...((((.(((........))).))))....))).................(((((((((((....))))))))))))))))........- ( -28.70)
>DroSim_CAF1 26337 102 - 1
UGCCGGCUGCCACUAAUUAAUUGCAAACUAAAUGAGUUUCUCGGCAUAAAACUUUAUCCACAGCAAAGCUGAUUGCUGUCAGUUUUGCGGCCGAAGGAGGAG
...((((((((...((((.(((........))).))))....))).................(((((((((((....))))))))))))))))......... ( -28.70)
>DroEre_CAF1 28309 102 - 1
UGCCGGCUGCCACUAAUUAAUUGCAAACUAAAUGAGUUUCUCGGCAUAAAACUUUAUCCACAGCAAAGCUGAUUGCUGUCAGUUUUGCGGCCGAAGAAGGAG
...((((((((...((((.(((........))).))))....))).................(((((((((((....))))))))))))))))......... ( -28.70)
>DroYak_CAF1 25994 101 - 1
-NNNNNCUGCCACUAAUUAAUUGCAAACUAAAUGAGUUUCUCGGCAUAAAACUUUAUCCACAGCAAAGCUGAUUGCUGUCAGUUUUGCGGCAAAAGGCGGAG
-.....(((((..........((((((((.....)))))....)))................(((((((((((....))))))))))).......))))).. ( -26.90)
>consensus
UGCCGGCUGCCACUAAUUAAUUGCAAACUAAAUGAGUUUCUCGGCAUAAAACUUUAUCCACAGCAAAGCUGAUUGCUGUCAGUUUUGCGGCCGAAGGAGGAG
...((((((((...((((.(((........))).))))....))).................(((((((((((....))))))))))))))))......... (-25.90 = -26.50 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:17 2006