Locus 7930

Sequence ID	3R_DroMel_CAF1
Location	21,257,453 – 21,257,616
Length	163
Max. P	0.999119

overview

Window 4

Location	21,257,453 – 21,257,558
Length	105
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	72.23
Mean single sequence MFE	-22.17
Consensus MFE	-10.06
Energy contribution	-10.42
Covariance contribution	0.36
Combinations/Pair	1.26
Mean z-score	-2.14
Structure conservation index	0.45
SVM decision value	1.60
SVM RNA-class probability	0.967067
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21257453 105 + 27905053
U-----UGUCAUCGUUUUGGCUUUUGUUUUCUUGAUUUUC-UUUCGGGCC---GU------CUUUUCCGCCCCACUGCCACAGCCUGUCUGUCCUAAACAAAUAACUUUUCGAUGGCAUU
.-----((((((((....(...(((((((...........-....((((.---(.------.....).)))).......((((.....))))...)))))))...)....)))))))).. ( -23.70)
>DroSec_CAF1 82396 105 + 1
U-----UGUCAUCGUUUUGGCUUUUGUUUUCUUGAUUUUC-UUUCGGGCC---GU------CUUUUCCGCCCCAGUGCCACAGCCUGUCUGUCCUAAACAAAUAACUUUUCGAUGGCAUU
.-----((((((((....(...(((((((....(((....-....((((.---(.------.....).))))(((.((....)))))...)))..)))))))...)....)))))))).. ( -26.70)
>DroWil_CAF1 84908 108 + 1
CAUCAACGUCAUUAUCUUCUAAUUUGUUUUCAGAAUA-UC-AAUAGAGAA---GUAAAAUUCCAUUCCGUUCU-UUGUC---GCUU---UUCACUUUUCACAUAACUUUUCAAUGGCAUU
.......((((((.........((((....))))...-..-....(((((---((.(((..(.((........-..)).---)..)---)).)))))))............))))))... ( -11.80)
>DroYak_CAF1 91877 104 + 1
U-----UGUCAUCAUUUU-GCUUUUGUUUUCUUGAUUUUC-UUUAGGGUC---GU------CUUUUCCGCCCCAGUGCCACAGCCUGUCUGUCCUAAACAAAUAACUUUUCGAUGGCAUU
.-----(((((((.....-...(((((((....(((....-....((((.---(.------.....).))))(((.((....)))))...)))..))))))).........))))))).. ( -20.83)
>DroAna_CAF1 76372 105 + 1
U-----UGUCAUCAUUU-GCUCUUUGUUUUCUUGAUGCCAUUUUUGGGCCGGCGU------CGCUUUCGCCCCAGUGACAC---CAGCCUGUCCUAAACAAAUAACUUUCCGAUGGCAUU
.-----(((((((....-....(((((((....(((.........((((.((.((------((((........)))))).)---).)))))))..))))))).........))))))).. ( -27.83)
>consensus
U_____UGUCAUCAUUUUGGCUUUUGUUUUCUUGAUUUUC_UUUAGGGCC___GU______CUUUUCCGCCCCAGUGCCACAGCCUGUCUGUCCUAAACAAAUAACUUUUCGAUGGCAUU
.......((((((.........(((((((................((((...................))))....((....))...........))))))).........))))))... (-10.06 = -10.42 +   0.36)

alignment

secondary structure

dotplot

Window 5

Location	21,257,453 – 21,257,558
Length	105
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	72.23
Mean single sequence MFE	-23.80
Consensus MFE	-8.64
Energy contribution	-10.20
Covariance contribution	1.56
Combinations/Pair	1.18
Mean z-score	-1.91
Structure conservation index	0.36
SVM decision value	0.76
SVM RNA-class probability	0.843091
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21257453 105 - 27905053
AAUGCCAUCGAAAAGUUAUUUGUUUAGGACAGACAGGCUGUGGCAGUGGGGCGGAAAAG------AC---GGCCCGAAA-GAAAAUCAAGAAAACAAAAGCCAAAACGAUGACA-----A
..((.(((((...((((.((((((...))))))..)))).((((...(((.((......------.)---).)))((..-.....))............))))...))))).))-----. ( -25.30)
>DroSec_CAF1 82396 105 - 1
AAUGCCAUCGAAAAGUUAUUUGUUUAGGACAGACAGGCUGUGGCACUGGGGCGGAAAAG------AC---GGCCCGAAA-GAAAAUCAAGAAAACAAAAGCCAAAACGAUGACA-----A
..((.(((((....(((.(((((((........(((((....)).)))((((.(.....------.)---.))))....-...........)))))))))).....))))).))-----. ( -25.30)
>DroWil_CAF1 84908 108 - 1
AAUGCCAUUGAAAAGUUAUGUGAAAAGUGAA---AAGC---GACAA-AGAACGGAAUGGAAUUUUAC---UUCUCUAUU-GA-UAUUCUGAAAACAAAUUAGAAGAUAAUGACGUUGAUG
.....(((..(...(((((..((.(((((((---(..(---.....-...........)..))))))---)).))....-..-..((((((.......))))))....))))).)..))) ( -14.49)
>DroYak_CAF1 91877 104 - 1
AAUGCCAUCGAAAAGUUAUUUGUUUAGGACAGACAGGCUGUGGCACUGGGGCGGAAAAG------AC---GACCCUAAA-GAAAAUCAAGAAAACAAAAGC-AAAAUGAUGACA-----A
..((.(((((....(((.(((((((........(((((....)).)))(((((......------.)---).)))....-...........))))))))))-....))))).))-----. ( -21.70)
>DroAna_CAF1 76372 105 - 1
AAUGCCAUCGGAAAGUUAUUUGUUUAGGACAGGCUG---GUGUCACUGGGGCGAAAGCG------ACGCCGGCCCAAAAAUGGCAUCAAGAAAACAAAGAGC-AAAUGAUGACA-----A
..((.(((((....(((.(((((((......(((((---(((((......((....)))------)))))))))((....)).........))))))).)))-...))))).))-----. ( -32.20)
>consensus
AAUGCCAUCGAAAAGUUAUUUGUUUAGGACAGACAGGCUGUGGCACUGGGGCGGAAAAG______AC___GGCCCGAAA_GAAAAUCAAGAAAACAAAAGCCAAAAUGAUGACA_____A
..((.(((((........(((((((...((((.....)))).......((((...................))))................)))))))........))))).))...... ( -8.64 = -10.20 +   1.56)

alignment

secondary structure

dotplot

Window 6

Location	21,257,488 – 21,257,581
Length	93
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	89.96
Mean single sequence MFE	-27.32
Consensus MFE	-18.34
Energy contribution	-19.62
Covariance contribution	1.28
Combinations/Pair	1.04
Mean z-score	-2.62
Structure conservation index	0.67
SVM decision value	0.18
SVM RNA-class probability	0.622514
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21257488 93 - 27905053
AAUGAAUGAAUAACUUUUUAGUCAAUGCCAUCGAAAAGUUAUUUGUUUAGGACAGACAGGCUGUGGCAGUGGGGCGGAAAAGAC---GGCCCGAAA-
..((((..((((((((((..((.......))..))))))))))..))))..((((.....)))).....((((.((.......)---).))))...- ( -25.80)
>DroSec_CAF1 82431 93 - 1
AAUGAAUGAAUAACUUUUUAGUCAAUGCCAUCGAAAAGUUAUUUGUUUAGGACAGACAGGCUGUGGCACUGGGGCGGAAAAGAC---GGCCCGAAA-
..((((..((((((((((..((.......))..))))))))))..)))).......(((((....)).)))((((.(......)---.))))....- ( -27.50)
>DroSim_CAF1 85167 93 - 1
AAUGAAUGAAUAACUUUUUAGUCAAUGCCAUCGAAAAGUUAUUUGCUUAGGACAGACAGGCUGUGGCACUGGGGCGGAAAAGAC---GGCCCGAAA-
..(((..(((((((((((..((.......))..)))))))))))..))).......(((((....)).)))((((.(......)---.))))....- ( -24.30)
>DroYak_CAF1 91911 93 - 1
AAUGAAUGAAUAACUUUUUAGUCAAUGCCAUCGAAAAGUUAUUUGUUUAGGACAGACAGGCUGUGGCACUGGGGCGGAAAAGAC---GACCCUAAA-
..((((..((((((((((..((.......))..))))))))))..)))).......(((((....)).)))(((((.......)---).)))....- ( -25.00)
>DroAna_CAF1 76406 90 - 1
AAU----GAAUAACUUUCUAGUCAAUGCCAUCGGAAAGUUAUUUGUUUAGGACAGGCUG---GUGUCACUGGGGCGAAAGCGACGCCGGCCCAAAAA
((.----.((((((((((..((.......))..))))))))))..)).......(((((---(((((......((....))))))))))))...... ( -34.00)
>consensus
AAUGAAUGAAUAACUUUUUAGUCAAUGCCAUCGAAAAGUUAUUUGUUUAGGACAGACAGGCUGUGGCACUGGGGCGGAAAAGAC___GGCCCGAAA_
..((((((((((((((((..((.......))..))))))))))))))))..((((.....)))).......((((.............))))..... (-18.34 = -19.62 +   1.28)

alignment

secondary structure

dotplot

Window 7

Location	21,257,518 – 21,257,616
Length	98
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	84.18
Mean single sequence MFE	-31.80
Consensus MFE	-26.16
Energy contribution	-26.04
Covariance contribution	-0.12
Combinations/Pair	1.17
Mean z-score	-3.50
Structure conservation index	0.82
SVM decision value	3.38
SVM RNA-class probability	0.999119
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21257518 98 - 27905053
GAGUGGCCUUAUUUGGGCAAAAACGUCUGGGCUGAAAUGAAUGAAUAACUUUUUAGUCAAUGCCAUCGAAAAGUUAUUUGUUUAGGACAGACAGGCUG
..((.((((.....))))....))(((((..(((...((((..((((((((((..((.......))..))))))))))..))))...))).))))).. ( -31.20)
>DroSec_CAF1 82461 98 - 1
GAGUGGCCCCAUUUGGGCCAAAACGUCUGGGCUGAAAUGAAUGAAUAACUUUUUAGUCAAUGCCAUCGAAAAGUUAUUUGUUUAGGACAGACAGGCUG
...((((((.....))))))....(((((..(((...((((..((((((((((..((.......))..))))))))))..))))...))).))))).. ( -36.00)
>DroSim_CAF1 85197 98 - 1
GAGUGGCCCCAUUUGGGCCAAAACGUCUGGGCUGAAAUGAAUGAAUAACUUUUUAGUCAAUGCCAUCGAAAAGUUAUUUGCUUAGGACAGACAGGCUG
...((((((.....))))))....(((((..(((...(((..(((((((((((..((.......))..)))))))))))..)))...))).))))).. ( -32.80)
>DroYak_CAF1 91941 98 - 1
GAGUGGCCUCAGUUGGGCCAAAAUGUCUGGGCUGAAAUGAAUGAAUAACUUUUUAGUCAAUGCCAUCGAAAAGUUAUUUGUUUAGGACAGACAGGCUG
...((((((.....))))))....(((((..(((...((((..((((((((((..((.......))..))))))))))..))))...))).))))).. ( -33.70)
>DroAna_CAF1 76440 77 - 1
GCGC--------------UGGCAUGUCUGGGUGGAAAU----GAAUAACUUUCUAGUCAAUGCCAUCGGAAAGUUAUUUGUUUAGGACAGGCUG---G
...(--------------..((.(((((......(((.----.((((((((((..((.......))..))))))))))..))).))))).))..---) ( -25.30)
>consensus
GAGUGGCCCCAUUUGGGCCAAAACGUCUGGGCUGAAAUGAAUGAAUAACUUUUUAGUCAAUGCCAUCGAAAAGUUAUUUGUUUAGGACAGACAGGCUG
...((((((.....))))))....(((((..(((((......(((((((((((..((.......))..))))))))))).)))))..)))))...... (-26.16 = -26.04 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:58:23 2006