Locus 7326

Sequence ID	2L_DroMel_CAF1
Location	20,473,221 – 20,473,380
Length	159
Max. P	0.851537

overview

Window 5

Location	20,473,221 – 20,473,341
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.75
Mean single sequence MFE	-24.76
Consensus MFE	-24.52
Energy contribution	-24.32
Covariance contribution	-0.20
Combinations/Pair	1.12
Mean z-score	-1.26
Structure conservation index	0.99
SVM decision value	0.71
SVM RNA-class probability	0.829529
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20473221 120 - 22407834
AACAUUCUUGGCAAUUAACAUUUAAAAUUCCCUGCAACGAAACAUAAUCGAAUUGUAAUGAAAAUCGUCAACGUGUCAGGUGAAAUGGCAAUCGUGAAUUUUAAUUAGCAAUUUGCUGAG
......((..((((.......(((((((((..((((((((.......)))..))))).............((((((((.......)))))..))))))))))))........))))..)) ( -22.16)
>DroSec_CAF1 26212 120 - 1
AACAUUCUUGGCAAUUAACAUUUAAAAUUCGCUGCAACGAAACAUAAUCGAAUUGUAAUGAAAAUCGUCAACGUGUCAGGUGAAAUGGCAAUCGUGAAUUUUAAUUAGCAAUUUGCUGGG
......((..((((.......(((((((((((((((((((.......)))..)))))................(((((.......)))))...)))))))))))........))))..)) ( -25.46)
>DroSim_CAF1 28178 120 - 1
AACAUUCUUGGCAAUUAACAUUUAAAAUUCGCUGCAACGAAACAUAAUCGAAUUGUAAUGAAAAUCGUCAACGUGUCAGGUGAAAUGGCAAUCGUGAAUUUUAAUUAGCAAUUUGCUGAG
......((..((((.......(((((((((((((((((((.......)))..)))))................(((((.......)))))...)))))))))))........))))..)) ( -25.46)
>DroEre_CAF1 28587 120 - 1
AACAUUCUUGGCAAUUAACAUUUAAAAUUCGCUGCAGCGAAACAUAAUCGAAUUGUAAUGAAAAUCGUCAACGUGUCAGGUGAAAUGGCAAUCGUGAAUUUUAAUUAGCAAUUUGCCGAG
......((((((((.......(((((((((((((((.(((.......)))...))))................(((((.......)))))...)))))))))))........)))))))) ( -28.06)
>DroYak_CAF1 25569 120 - 1
AACAUUCUUGGCAAUUAACAUUUAAAUUUCACUGCAACGAAACAUAAUCGAAUUGUAAUGAAAAUCGUCAACGUGUCAGAUGAAAUGGCAAUCGUGAAUUUUAAUUAGCAAUUUGCUGAG
......((..((((.......(((((.(((((((((((((.......)))..)))))................(((((.......)))))...))))).)))))........))))..)) ( -22.66)
>consensus
AACAUUCUUGGCAAUUAACAUUUAAAAUUCGCUGCAACGAAACAUAAUCGAAUUGUAAUGAAAAUCGUCAACGUGUCAGGUGAAAUGGCAAUCGUGAAUUUUAAUUAGCAAUUUGCUGAG
......((((((((.......(((((((((((((((((((.......)))..)))))................(((((.......)))))...)))))))))))........)))))))) (-24.52 = -24.32 +  -0.20)

alignment

secondary structure

dotplot

Window 6

Location	20,473,261 – 20,473,380
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.39
Mean single sequence MFE	-21.12
Consensus MFE	-20.14
Energy contribution	-20.66
Covariance contribution	0.52
Combinations/Pair	1.06
Mean z-score	-1.24
Structure conservation index	0.95
SVM decision value	0.79
SVM RNA-class probability	0.851537
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20473261 119 + 22407834
CCUGACACGUUGACGAUUUUCAUUACAAUUCGAUUAUGUUUCGUUGCAGGGAAUUUUAAAUGUUAAUUGCCAAGAAUGUUUCAACAAAUUCAUUUCUCAUUAAUGUGUCUU-UUCAUUUA
...(((((((((((((((..((((..(((((.....(((......)))..)))))...))))..)))))....((((..........))))........))))))))))..-........ ( -20.70)
>DroSec_CAF1 26252 119 + 1
CCUGACACGUUGACGAUUUUCAUUACAAUUCGAUUAUGUUUCGUUGCAGCGAAUUUUAAAUGUUAAUUGCCAAGAAUGUUUCAACAAAUUCAUUUUUCAUUAAUGUGUCUU-UUUAUUUA
...(((((((((((((((..((((..((((((....(((......))).))))))...))))..)))))..(((((((............)))))))..))))))))))..-........ ( -25.00)
>DroSim_CAF1 28218 120 + 1
CCUGACACGUUGACGAUUUUCAUUACAAUUCGAUUAUGUUUCGUUGCAGCGAAUUUUAAAUGUUAAUUGCCAAGAAUGUUUCAACAAAUUCAUUUCUCAUUAAUGUGUCUUUUUUAUUUA
...(((((((((((((((..((((..((((((....(((......))).))))))...))))..)))))....((((..........))))........))))))))))........... ( -24.60)
>DroEre_CAF1 28627 118 + 1
CCUGACACGUUGACGAUUUUCAUUACAAUUCGAUUAUGUUUCGCUGCAGCGAAUUUUAAAUGUUAAUUGCCAAGAAUGUUUCGACAAAUUCAUUUCUCAUUAGUGUUUCUU-UUUAU-UG
...(((((.(((.(((((..((((..((((((....(((......))).))))))...))))..))))).)))((((..........))))...........)))))....-.....-.. ( -19.90)
>DroYak_CAF1 25609 118 + 1
UCUGACACGUUGACGAUUUUCAUUACAAUUCGAUUAUGUUUCGUUGCAGUGAAAUUUAAAUGUUAAUUGCCAAGAAUGUUUCAACAAAUUCAUUUCUCAUUAAUGUUUCUU-UUUAU-UA
...((.(((((((.((.(((((((.(((..(((.......)))))).)))))))...................((((..........)))).....)).))))))).))..-.....-.. ( -15.40)
>consensus
CCUGACACGUUGACGAUUUUCAUUACAAUUCGAUUAUGUUUCGUUGCAGCGAAUUUUAAAUGUUAAUUGCCAAGAAUGUUUCAACAAAUUCAUUUCUCAUUAAUGUGUCUU_UUUAUUUA
...(((((((((((((((..((((..((((((....(((......))).))))))...))))..)))))....((((..........))))........))))))))))........... (-20.14 = -20.66 +   0.52)

alignment

secondary structure

dotplot

Window 7

Location	20,473,261 – 20,473,380
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.39
Mean single sequence MFE	-19.82
Consensus MFE	-18.64
Energy contribution	-19.00
Covariance contribution	0.36
Combinations/Pair	1.09
Mean z-score	-1.21
Structure conservation index	0.94
SVM decision value	0.57
SVM RNA-class probability	0.785312
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20473261 119 - 22407834
UAAAUGAA-AAGACACAUUAAUGAGAAAUGAAUUUGUUGAAACAUUCUUGGCAAUUAACAUUUAAAAUUCCCUGCAACGAAACAUAAUCGAAUUGUAAUGAAAAUCGUCAACGUGUCAGG
........-..(((((.((.((((.(((((...((((..(.......)..))))....)))))....(((..((((((((.......)))..)))))..)))..)))).)).)))))... ( -20.40)
>DroSec_CAF1 26252 119 - 1
UAAAUAAA-AAGACACAUUAAUGAAAAAUGAAUUUGUUGAAACAUUCUUGGCAAUUAACAUUUAAAAUUCGCUGCAACGAAACAUAAUCGAAUUGUAAUGAAAAUCGUCAACGUGUCAGG
........-..(((((.((.((((.(((((...((((..(.......)..))))....)))))....((((.((((((((.......)))..))))).))))..)))).)).)))))... ( -21.90)
>DroSim_CAF1 28218 120 - 1
UAAAUAAAAAAGACACAUUAAUGAGAAAUGAAUUUGUUGAAACAUUCUUGGCAAUUAACAUUUAAAAUUCGCUGCAACGAAACAUAAUCGAAUUGUAAUGAAAAUCGUCAACGUGUCAGG
...........(((((.((.((((.(((((...((((..(.......)..))))....)))))....((((.((((((((.......)))..))))).))))..)))).)).)))))... ( -22.00)
>DroEre_CAF1 28627 118 - 1
CA-AUAAA-AAGAAACACUAAUGAGAAAUGAAUUUGUCGAAACAUUCUUGGCAAUUAACAUUUAAAAUUCGCUGCAGCGAAACAUAAUCGAAUUGUAAUGAAAAUCGUCAACGUGUCAGG
..-.....-.....((((..((((.(((((...(((((((.......)))))))....)))))....((((.((((.(((.......)))...)))).))))..))))....)))).... ( -17.20)
>DroYak_CAF1 25609 118 - 1
UA-AUAAA-AAGAAACAUUAAUGAGAAAUGAAUUUGUUGAAACAUUCUUGGCAAUUAACAUUUAAAUUUCACUGCAACGAAACAUAAUCGAAUUGUAAUGAAAAUCGUCAACGUGUCAGA
..-.....-..((.((.((.((((.(((((...((((..(.......)..))))....)))))...(((((.((((((((.......)))..))))).))))).)))).)).)).))... ( -17.60)
>consensus
UAAAUAAA_AAGACACAUUAAUGAGAAAUGAAUUUGUUGAAACAUUCUUGGCAAUUAACAUUUAAAAUUCGCUGCAACGAAACAUAAUCGAAUUGUAAUGAAAAUCGUCAACGUGUCAGG
...........(((((.((.((((.(((((...(((((((.......)))))))....)))))....((((.((((((((.......)))..))))).))))..)))).)).)))))... (-18.64 = -19.00 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:41 2006