Locus 4193

Sequence ID	3R_DroMel_CAF1
Location	11,345,333 – 11,345,558
Length	225
Max. P	0.988230

overview

Window 4

Location	11,345,333 – 11,345,450
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.94
Mean single sequence MFE	-29.70
Consensus MFE	-25.98
Energy contribution	-26.46
Covariance contribution	0.48
Combinations/Pair	1.07
Mean z-score	-1.41
Structure conservation index	0.87
SVM decision value	0.55
SVM RNA-class probability	0.778856
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11345333 117 + 27905053
CUUUAUUGCAGUUUCAGCAGCAGCUCCUGCAUUGUCCCUGCUGUUAUCGCUGCUUUUCAAAUGACAUUUAAAUAUUUUCCACAAAGCCACAAGCUGUCAGGGAAUUUAGAAUAGUGG---
.......(((((...((((((((...(......)...))))))))...)))))...........((((....((..((((....(((.....))).....))))..))....)))).--- ( -28.20)
>DroSec_CAF1 84197 117 + 1
CUUUAUUGCAGUUUCAGCAGCAGCUCCUGCAUUGUCCCUGCUGUUAUCUCUGCUUUUCAAAUGACAUUUAAAUAUUUCCCACAAAGCCACAAGCUGUCAGGGAAUAUGGAAUAGUGG---
.......((((....((((((((...(......)...))))))))....))))...........((((....((((((((....(((.....)))....))))).)))....)))).--- ( -28.10)
>DroSim_CAF1 82743 117 + 1
CUUUAUUGCAGUUUCAGCAGCAGCUCCUGCAUUGUCCCUGCUGUUAUCGCUGCUUUUCAAAUGACAUUUAAAUAUUUCCCACAAAGCCACAAGCUGUCAGGGAAUAUGGAAUAGUGG---
.......(((((...((((((((...(......)...))))))))...)))))...........((((....((((((((....(((.....)))....))))).)))....)))).--- ( -29.50)
>DroEre_CAF1 80477 120 + 1
CUUUAUUGCAGUUUCAGCAGCAGCUUCUGCAUUGUCCCUGCUGUUAUCGCAGCUUUUCAAACGACAUUUAAAUAUUUCCCACAAAGCCACAAGCUGUCAGGGAAUAUGGAAUAGGGGGAC
......(((((....(((....))).)))))..(((((((((((....)))))............((((......(((((....(((.....)))....)))))....))))..)))))) ( -32.80)
>DroYak_CAF1 82590 117 + 1
CUUUAUUGCAGUUUCAGCAGCAGCUCCGGCAUUGUCCCUGCUGUUAUCGCUGCUUUUCAAAUGACAUUUAAAUAUUUCCCACAAAGCCACAAGCUGUCAGGGAAUAUGGAAUAGUGG---
.......(((((...((((((((....(((...))).))))))))...)))))...........((((....((((((((....(((.....)))....))))).)))....)))).--- ( -29.90)
>consensus
CUUUAUUGCAGUUUCAGCAGCAGCUCCUGCAUUGUCCCUGCUGUUAUCGCUGCUUUUCAAAUGACAUUUAAAUAUUUCCCACAAAGCCACAAGCUGUCAGGGAAUAUGGAAUAGUGG___
.......(((((...((((((((...(......)...))))))))...)))))...........((((....((((((((....(((.....)))....))))).)))....)))).... (-25.98 = -26.46 +   0.48)

alignment

secondary structure

dotplot

Window 5

Location	11,345,413 – 11,345,519
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.50
Mean single sequence MFE	-35.52
Consensus MFE	-26.59
Energy contribution	-27.23
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.63
Structure conservation index	0.75
SVM decision value	0.07
SVM RNA-class probability	0.570005
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11345413 106 + 27905053
ACAAAGCCACAAGCUGUCAGGGAAUUUAGAAUAGUGG------CAGUAUGCCCAGGAC--------UAAGGACACUCCUGCCACAAGGAGCUGUGAAGAUGCUGUCGGUCUGACAGCGCA
............(((((((((..(((......)))((------((((((..((.....--------...))((((((((......))))).)))....))))))))..)))))))))... ( -33.90)
>DroSec_CAF1 84277 106 + 1
ACAAAGCCACAAGCUGUCAGGGAAUAUGGAAUAGUGG------GAAUAUGGCCAGGAC--------UAAGGACGCUCCUGCCACAAGGAGCUGUGAAGAUGCUGUCGGUCUGACAGCGCA
.....((((((....(((..((....(((.(((....------...)))..)))...)--------)...)))((((((......)))))))))).....((((((.....)))))))). ( -32.70)
>DroSim_CAF1 82823 106 + 1
ACAAAGCCACAAGCUGUCAGGGAAUAUGGAAUAGUGG------GAAUACGGCCAGGAC--------UAAGGACGCUCCUGCCACAAGGAGCUGUAAAGAUGCUGUCGGUCUGACAGCGCA
............(((((((((.....(((....(((.------...)))..)))....--------....(((((((((......)))))).(((....))).)))..)))))))))... ( -33.00)
>DroEre_CAF1 80557 120 + 1
ACAAAGCCACAAGCUGUCAGGGAAUAUGGAAUAGGGGGACCAGGAAUAUGGCCAGGACUCCUGGCCUAAGGAUGCUCCUGCCACAAGGAGCUGUGAAGAUGCUGUCGGUCUGACAGCGCA
.....((((((....(((...............((....))........(((((((...)))))))....)))((((((......)))))))))).....((((((.....)))))))). ( -44.60)
>DroYak_CAF1 82670 106 + 1
ACAAAGCCACAAGCUGUCAGGGAAUAUGGAAUAGUGG------GAAUAUGGCCAGGAC--------CAAGGAUGCUCCUGCCACAAGGAGCUGUGAAGAUGCUGUCGCUCUGACAGCGCA
............((((((((((...((((.(((((..------.....((((.((((.--------((....)).))))))))......))))).......))))..))))))))))... ( -33.42)
>consensus
ACAAAGCCACAAGCUGUCAGGGAAUAUGGAAUAGUGG______GAAUAUGGCCAGGAC________UAAGGACGCUCCUGCCACAAGGAGCUGUGAAGAUGCUGUCGGUCUGACAGCGCA
.....((((((....(((..((.((((..................))))..))..)))...............((((((......)))))))))).....((((((.....)))))))). (-26.59 = -27.23 +   0.64)

alignment

secondary structure

dotplot

Window 6

Location	11,345,413 – 11,345,519
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.50
Mean single sequence MFE	-33.36
Consensus MFE	-27.07
Energy contribution	-26.99
Covariance contribution	-0.08
Combinations/Pair	1.11
Mean z-score	-1.67
Structure conservation index	0.81
SVM decision value	0.71
SVM RNA-class probability	0.829808
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11345413 106 - 27905053
UGCGCUGUCAGACCGACAGCAUCUUCACAGCUCCUUGUGGCAGGAGUGUCCUUA--------GUCCUGGGCAUACUG------CCACUAUUCUAAAUUCCCUGACAGCUUGUGGCUUUGU
.((((((((.....)))))).....(((((((....(((((((..((((((...--------.....)))))).)))------))))...((..........)).))).))))))..... ( -38.60)
>DroSec_CAF1 84277 106 - 1
UGCGCUGUCAGACCGACAGCAUCUUCACAGCUCCUUGUGGCAGGAGCGUCCUUA--------GUCCUGGCCAUAUUC------CCACUAUUCCAUAUUCCCUGACAGCUUGUGGCUUUGU
.((((((((.....)))))).....(((((((...((((((((((.(.......--------))))).))))))...------.........((.......))..))).))))))..... ( -28.90)
>DroSim_CAF1 82823 106 - 1
UGCGCUGUCAGACCGACAGCAUCUUUACAGCUCCUUGUGGCAGGAGCGUCCUUA--------GUCCUGGCCGUAUUC------CCACUAUUCCAUAUUCCCUGACAGCUUGUGGCUUUGU
.((((((((.....)))))).....((((((((((......)))))).......--------(((..((..((((..------..........))))..)).)))....))))))..... ( -27.20)
>DroEre_CAF1 80557 120 - 1
UGCGCUGUCAGACCGACAGCAUCUUCACAGCUCCUUGUGGCAGGAGCAUCCUUAGGCCAGGAGUCCUGGCCAUAUUCCUGGUCCCCCUAUUCCAUAUUCCCUGACAGCUUGUGGCUUUGU
.((((((((.....)))))).....((((((((((......)))))).......(((((((...))))))).......(((..........)))...............))))))..... ( -39.30)
>DroYak_CAF1 82670 106 - 1
UGCGCUGUCAGAGCGACAGCAUCUUCACAGCUCCUUGUGGCAGGAGCAUCCUUG--------GUCCUGGCCAUAUUC------CCACUAUUCCAUAUUCCCUGACAGCUUGUGGCUUUGU
...((((((((.((....))...............((((((((((.((....))--------.)))).))))))...------.................))))))))............ ( -32.80)
>consensus
UGCGCUGUCAGACCGACAGCAUCUUCACAGCUCCUUGUGGCAGGAGCGUCCUUA________GUCCUGGCCAUAUUC______CCACUAUUCCAUAUUCCCUGACAGCUUGUGGCUUUGU
.((((((((.....)))))).....((((((((((......))))))...............(((..((..((((..................))))..)).)))....))))))..... (-27.07 = -26.99 +  -0.08)

alignment

secondary structure

dotplot

Window 7

Location	11,345,450 – 11,345,558
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.57
Mean single sequence MFE	-42.46
Consensus MFE	-36.20
Energy contribution	-36.96
Covariance contribution	0.76
Combinations/Pair	1.06
Mean z-score	-1.87
Structure conservation index	0.85
SVM decision value	1.51
SVM RNA-class probability	0.959876
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11345450 108 + 27905053
---CAGUAUGCCCAGGAC--------UAAGGACACUCCUGCCACAAGGAGCUGUGAAGAUGCUGUCGGUCUGACAGCGCACAAAGCUCAAAUUAGUGGCGGCCUCGCCCUCGGCCGUCG-
---............(((--------..(((.....)))(((((((.((((((((....(((((((.....))))))))))..)))))...)).)))))((((........))))))).- ( -39.70)
>DroSec_CAF1 84314 108 + 1
---GAAUAUGGCCAGGAC--------UAAGGACGCUCCUGCCACAAGGAGCUGUGAAGAUGCUGUCGGUCUGACAGCGCACAAAGCUCAAAUUAGUGGCAACCUCGCCCUCGGCCGUCG-
---....(((((((((..--------..(((.....)))(((((((.((((((((....(((((((.....))))))))))..)))))...)).)))))........))).))))))..- ( -42.20)
>DroSim_CAF1 82860 108 + 1
---GAAUACGGCCAGGAC--------UAAGGACGCUCCUGCCACAAGGAGCUGUAAAGAUGCUGUCGGUCUGACAGCGCACAAAGCUCAAAUUAGUGGCAACCUCGCCCUCGGCCGUCG-
---....(((((((((..--------..(((.....)))(((((((.(((((.....(.(((((((.....))))))))....)))))...)).)))))........))).))))))..- ( -43.30)
>DroEre_CAF1 80597 119 + 1
CAGGAAUAUGGCCAGGACUCCUGGCCUAAGGAUGCUCCUGCCACAAGGAGCUGUGAAGAUGCUGUCGGUCUGACAGCGCACAAAGCUCAAAUUAGUGGUGGCCUCGCCCUCG-CCCUCGG
.(((.....(((((((...)))))))..(((..((((((......)))))).((((....((((((.....))))))((.((..(((......)))..)))).)))))))..-.)))... ( -44.80)
>DroYak_CAF1 82707 109 + 1
---GAAUAUGGCCAGGAC--------CAAGGAUGCUCCUGCCACAAGGAGCUGUGAAGAUGCUGUCGCUCUGACAGCGCACAAAGCUCAAAUUAGUGGCGGCCUCGCCCUCGGCACUCGG
---......((((((((.--------((....)).))))(((((((.((((((((....(((((((.....))))))))))..)))))...)).)))))))))..(((...)))...... ( -42.30)
>consensus
___GAAUAUGGCCAGGAC________UAAGGACGCUCCUGCCACAAGGAGCUGUGAAGAUGCUGUCGGUCUGACAGCGCACAAAGCUCAAAUUAGUGGCGGCCUCGCCCUCGGCCGUCG_
.......(((((((((............(((.....)))(((((((.(((((.....(.(((((((.....))))))))....)))))...)).)))))........))).))))))... (-36.20 = -36.96 +   0.76)

alignment

secondary structure

dotplot

Window 8

Location	11,345,450 – 11,345,558
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.57
Mean single sequence MFE	-46.24
Consensus MFE	-38.14
Energy contribution	-38.78
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-2.31
Structure conservation index	0.82
SVM decision value	2.11
SVM RNA-class probability	0.988230
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11345450 108 - 27905053
-CGACGGCCGAGGGCGAGGCCGCCACUAAUUUGAGCUUUGUGCGCUGUCAGACCGACAGCAUCUUCACAGCUCCUUGUGGCAGGAGUGUCCUUA--------GUCCUGGGCAUACUG---
-.....(((.((((((((((((((((......(((((.((...((((((.....)))))).....)).)))))...))))).)).....)))).--------))))).)))......--- ( -44.70)
>DroSec_CAF1 84314 108 - 1
-CGACGGCCGAGGGCGAGGUUGCCACUAAUUUGAGCUUUGUGCGCUGUCAGACCGACAGCAUCUUCACAGCUCCUUGUGGCAGGAGCGUCCUUA--------GUCCUGGCCAUAUUC---
-....((((.((((((((((((((((......(((((.((...((((((.....)))))).....)).)))))...)))))))......)))).--------)))))))))......--- ( -45.50)
>DroSim_CAF1 82860 108 - 1
-CGACGGCCGAGGGCGAGGUUGCCACUAAUUUGAGCUUUGUGCGCUGUCAGACCGACAGCAUCUUUACAGCUCCUUGUGGCAGGAGCGUCCUUA--------GUCCUGGCCGUAUUC---
-..((((((.((((((((((((((((......(((((.((...((((((.....)))))).....)).)))))...)))))))......)))).--------)))))))))))....--- ( -46.90)
>DroEre_CAF1 80597 119 - 1
CCGAGGG-CGAGGGCGAGGCCACCACUAAUUUGAGCUUUGUGCGCUGUCAGACCGACAGCAUCUUCACAGCUCCUUGUGGCAGGAGCAUCCUUAGGCCAGGAGUCCUGGCCAUAUUCCUG
..(((((-.(((((((((((((.........)).)))))))..((((((.....))))))..))))...((((((......)))))).))))).(((((((...)))))))......... ( -49.30)
>DroYak_CAF1 82707 109 - 1
CCGAGUGCCGAGGGCGAGGCCGCCACUAAUUUGAGCUUUGUGCGCUGUCAGAGCGACAGCAUCUUCACAGCUCCUUGUGGCAGGAGCAUCCUUG--------GUCCUGGCCAUAUUC---
..(((((((...)))..(((((((((......(((((.((...((((((.....)))))).....)).)))))...)))))((((.((....))--------.))))))))..))))--- ( -44.80)
>consensus
_CGACGGCCGAGGGCGAGGCCGCCACUAAUUUGAGCUUUGUGCGCUGUCAGACCGACAGCAUCUUCACAGCUCCUUGUGGCAGGAGCGUCCUUA________GUCCUGGCCAUAUUC___
.....((((.(((((......(((((......(((((.((...((((((.....)))))).....)).)))))...)))))(((.....)))..........)))))))))......... (-38.14 = -38.78 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:12 2006