Locus 9021

Sequence ID	3R_DroMel_CAF1
Location	24,171,805 – 24,171,935
Length	130
Max. P	0.986736

overview

Window 1

Location	24,171,805 – 24,171,895
Length	90
Sequences	5
Columns	90
Reading direction	forward
Mean pairwise identity	86.93
Mean single sequence MFE	-29.96
Consensus MFE	-21.52
Energy contribution	-21.04
Covariance contribution	-0.48
Combinations/Pair	1.12
Mean z-score	-2.94
Structure conservation index	0.72
SVM decision value	1.65
SVM RNA-class probability	0.969959
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24171805 90 + 27905053
UUAGGCUGUGGGUUGUUGUUGUGGCUGCCGUUGCAAGCGGCAGGUGCAGCAUUCCACAGAAAGAAAUUUUGUAAGAAAUAUCUAUAUCUA
.(((((((((((....(((((((.(((((((.....))))))).))))))).)))))))..(((.(((((....))))).)))...)))) ( -35.60)
>DroSec_CAF1 12417 89 + 1
UUGGGCUGUGGGUUGUUGUUA-GGCUGCCGUUGCAAGUUGCAGGUGCAGCAUUCCACAGAAAGAAAAUAUGUCAGAAAAUUCCAAAUCUU
(((((((((((..((((((..-(.((((..(.....)..)))).)))))))..))))))...((.......)).......)))))..... ( -24.30)
>DroSim_CAF1 12357 90 + 1
UUGGGCUGUGGGUUGUUGUUGCGGCUGCCGUUGCAAGUUGCAGGUGCAGCAUUCCACAGAAAGAAAAUAUGUCAGAAAAUUCUAAAUCUA
(((((((((((..(((((((((((((((....)).)))))))...))))))..))))))...((.......)).......)))))..... ( -27.60)
>DroEre_CAF1 5686 87 + 1
UUGGGCUGUGGGUUGUUGU---GGCUGUCGUUGCAAGUUGCAGGUGCAGCAUUCCACAGAAAACAAAUGUGGCAUAAAAUGCAAUAUCUA
(((..((((((..((((((---(.((((..(.....)..)))).)))))))..))))))....)))((((.((((...)))).))))... ( -28.10)
>DroYak_CAF1 5942 87 + 1
UUGGGCUGUGGGUUGUUGU---GGCUGUCGUUGCAAGCUGCAGGUGCAGCAUUCCACAGCAAGAAAAUGUGGCAUAAAAUGCAAUACCUA
..(((((((((..((((((---(.((((.((.....)).)))).)))))))..)))))))...........((((...))))....)).. ( -34.20)
>consensus
UUGGGCUGUGGGUUGUUGUU__GGCUGCCGUUGCAAGUUGCAGGUGCAGCAUUCCACAGAAAGAAAAUAUGUCAGAAAAUUCAAUAUCUA
.....((((((..((((((....((.((........)).))....))))))..))))))............................... (-21.52 = -21.04 +  -0.48)

alignment

secondary structure

dotplot

Window 2

Location	24,171,805 – 24,171,895
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	86.93
Mean single sequence MFE	-19.73
Consensus MFE	-14.72
Energy contribution	-15.12
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.91
Structure conservation index	0.75
SVM decision value	0.55
SVM RNA-class probability	0.779854
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24171805 90 - 27905053
UAGAUAUAGAUAUUUCUUACAAAAUUUCUUUCUGUGGAAUGCUGCACCUGCCGCUUGCAACGGCAGCCACAACAACAACCCACAGCCUAA
(((....(((.((((......)))).)))..((((((..((.((...((((((.......))))))......)).))..)))))).))). ( -19.20)
>DroSec_CAF1 12417 89 - 1
AAGAUUUGGAAUUUUCUGACAUAUUUUCUUUCUGUGGAAUGCUGCACCUGCAACUUGCAACGGCAGCC-UAACAACAACCCACAGCCCAA
.....(..((....))..)............((((((...(((((...(((.....)))...))))).-..........))))))..... ( -18.34)
>DroSim_CAF1 12357 90 - 1
UAGAUUUAGAAUUUUCUGACAUAUUUUCUUUCUGUGGAAUGCUGCACCUGCAACUUGCAACGGCAGCCGCAACAACAACCCACAGCCCAA
.....(((((....)))))............((((((...(((((...(((.....)))...))))).(......)...))))))..... ( -20.40)
>DroEre_CAF1 5686 87 - 1
UAGAUAUUGCAUUUUAUGCCACAUUUGUUUUCUGUGGAAUGCUGCACCUGCAACUUGCAACGACAGCC---ACAACAACCCACAGCCCAA
(((((...((((...))))...)))))....((((((...((((....(((.....)))....)))).---........))))))..... ( -14.70)
>DroYak_CAF1 5942 87 - 1
UAGGUAUUGCAUUUUAUGCCACAUUUUCUUGCUGUGGAAUGCUGCACCUGCAGCUUGCAACGACAGCC---ACAACAACCCACAGCCCAA
..(((((........)))))..........(((((((...(((((....)))))..((.......)).---........))))))).... ( -26.00)
>consensus
UAGAUAUAGAAUUUUCUGACACAUUUUCUUUCUGUGGAAUGCUGCACCUGCAACUUGCAACGGCAGCC__AACAACAACCCACAGCCCAA
...............................((((((...(((((...(((.....)))...)))))............))))))..... (-14.72 = -15.12 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	24,171,821 – 24,171,935
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	76.54
Mean single sequence MFE	-29.15
Consensus MFE	-14.69
Energy contribution	-13.93
Covariance contribution	-0.76
Combinations/Pair	1.18
Mean z-score	-2.46
Structure conservation index	0.50
SVM decision value	2.05
SVM RNA-class probability	0.986736
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24171821 114 + 27905053
UGUUGUGGCUGCCGUUGCAAGCGGCAGGUGCAGCAUUCCACAGAAAGAAAUUUUGUAAGAAAUAUCUAUAUCUAGAAGGUGAGUAUAUAAUGCAUUAUUAUGCAUGACACCAAG
(((((((.(((((((.....))))))).)))))))(((.((((((.....))))))..)))...((((....)))).((((........((((((....))))))..))))... ( -34.50)
>DroSec_CAF1 12433 110 + 1
UGUUA-GGCUGCCGUUGCAAGUUGCAGGUGCAGCAUUCCACAGAAAGAAAAUAUGUCAGAAAAUUCCAAAUCUUGAACGGGAGUAUAUUAUGCAUA---CGGAAUGACACAAAA
(((((-.....((((((((.(((((....)))))(((((.....((((......................)))).....)))))......)))).)---)))..)))))..... ( -25.25)
>DroSim_CAF1 12373 111 + 1
UGUUGCGGCUGCCGUUGCAAGUUGCAGGUGCAGCAUUCCACAGAAAGAAAAUAUGUCAGAAAAUUCUAAAUCUAGAAUGGGAGUAUAUGAUGCAUA---CGGAAUGACACAAAA
..((((((((((....)).))))))))(((...((((((................((.....((((((....))))))..))((((.......)))---))))))).))).... ( -25.90)
>DroEre_CAF1 5702 90 + 1
UGU---GGCUGUCGUUGCAAGUUGCAGGUGCAGCAUUCCACAGAAAACAAAUGUGGCAUAAAAUGCAAUAUCUAGA------------------UA---UGGAUUGCUACAAAA
(((---(((....((((((.(((((....)))))...(((((.........))))).......))))))(((((..------------------..---))))).))))))... ( -27.60)
>DroYak_CAF1 5958 108 + 1
UGU---GGCUGUCGUUGCAAGCUGCAGGUGCAGCAUUCCACAGCAAGAAAAUGUGGCAUAAAAUGCAAUACCUAGAAAGGGAGUAUAUUAUGGACA---UGGAAUGCUACAAAA
(((---(((((((((((((.(((((....)))))...(((((.........))))).......)))))).(((....)))............))))---......))))))... ( -32.50)
>consensus
UGUU__GGCUGCCGUUGCAAGUUGCAGGUGCAGCAUUCCACAGAAAGAAAAUAUGUCAGAAAAUUCAAUAUCUAGAA_GGGAGUAUAUUAUGCAUA___CGGAAUGACACAAAA
(((....(((((..((((.....))))..))))).....)))...........(((((..............................................)))))..... (-14.69 = -13.93 +  -0.76)

alignment

secondary structure

dotplot

Window 4

Location	24,171,821 – 24,171,935
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	76.54
Mean single sequence MFE	-23.96
Consensus MFE	-10.77
Energy contribution	-11.53
Covariance contribution	0.76
Combinations/Pair	1.12
Mean z-score	-1.97
Structure conservation index	0.45
SVM decision value	0.52
SVM RNA-class probability	0.768978
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24171821 114 - 27905053
CUUGGUGUCAUGCAUAAUAAUGCAUUAUAUACUCACCUUCUAGAUAUAGAUAUUUCUUACAAAAUUUCUUUCUGUGGAAUGCUGCACCUGCCGCUUGCAACGGCAGCCACAACA
....((((.((((((....)))))).)))).....((...((((...(((.((((......)))).))).)))).))...(((((...(((.....)))...)))))....... ( -24.00)
>DroSec_CAF1 12433 110 - 1
UUUUGUGUCAUUCCG---UAUGCAUAAUAUACUCCCGUUCAAGAUUUGGAAUUUUCUGACAUAUUUUCUUUCUGUGGAAUGCUGCACCUGCAACUUGCAACGGCAGCC-UAACA
...((((((((((((---((((.....)))))...(......)....)))).....)))))))..((((......)))).(((((...(((.....)))...))))).-..... ( -23.00)
>DroSim_CAF1 12373 111 - 1
UUUUGUGUCAUUCCG---UAUGCAUCAUAUACUCCCAUUCUAGAUUUAGAAUUUUCUGACAUAUUUUCUUUCUGUGGAAUGCUGCACCUGCAACUUGCAACGGCAGCCGCAACA
..(((((..((((((---((((.....)))))........((((...((((..(........)..)))).)))).)))))(((((...(((.....)))...)))))))))).. ( -25.20)
>DroEre_CAF1 5702 90 - 1
UUUUGUAGCAAUCCA---UA------------------UCUAGAUAUUGCAUUUUAUGCCACAUUUGUUUUCUGUGGAAUGCUGCACCUGCAACUUGCAACGACAGCC---ACA
...(((((((.((((---((------------------...(((((..((((...))))......)))))..)))))).)))))))..(((.....))).........---... ( -21.40)
>DroYak_CAF1 5958 108 - 1
UUUUGUAGCAUUCCA---UGUCCAUAAUAUACUCCCUUUCUAGGUAUUGCAUUUUAUGCCACAUUUUCUUGCUGUGGAAUGCUGCACCUGCAGCUUGCAACGACAGCC---ACA
...((((((((((((---(.......................(((((........))))).((......))..)))))))))))))..(((.....))).........---... ( -26.20)
>consensus
UUUUGUGUCAUUCCA___UAUGCAUAAUAUACUCCC_UUCUAGAUAUAGAAUUUUCUGACACAUUUUCUUUCUGUGGAAUGCUGCACCUGCAACUUGCAACGGCAGCC__AACA
...(((((((..............................................)))))))..........((.....(((((...(((.....)))...)))))....)). (-10.77 = -11.53 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:24:58 2006