Locus 4589

Sequence ID	2L_DroMel_CAF1
Location	13,142,820 – 13,143,008
Length	188
Max. P	0.915613

overview

Window 8

Location	13,142,820 – 13,142,937
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.11
Mean single sequence MFE	-32.60
Consensus MFE	-23.08
Energy contribution	-23.76
Covariance contribution	0.68
Combinations/Pair	1.19
Mean z-score	-1.67
Structure conservation index	0.71
SVM decision value	0.07
SVM RNA-class probability	0.567820
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13142820 117 + 22407834
AUAGAUUAAUCCAAACAGCACCAGCAGUCGGAGAAUGGAUUGCAUUUUUCUUUCGAUUAGCUCUGGCUACAGUUGACUGAAUGUCAGUCGGCUCUUGAGCUGGGCUUUUAUAGCCUU---
................(((.(((((((((((((....(((((.(........))))))..))))))))..(((((((((.....))))))))).....))))))))...........--- ( -37.10)
>DroSec_CAF1 9891 117 + 1
AUAGAUUAAUCCAAACAGCACCAGCAGUCGGAGAAUGGAUUGCAUUUUUCUUUCGAUUAGCUCUGGCUACAGUUGACUGAAUGUCAGUCGGCUCUUGAGCUUGGCUUUUAUAGCCUU---
.((((((((((......((....))....((((((((.....))))))))....)))))).))))(((..(((((((((.....)))))))))....)))..((((.....))))..--- ( -34.20)
>DroSim_CAF1 10695 117 + 1
AUAGAUUAAUCCAAACAGCACCAGCAGUCGGAGAAUGGAUUGCAUUUUUCUUUCGAUUAGCUCUGGCUACAGUUGACUGAAUGUCAGUCGGCUCUUGAGCUUGGCUUUUAUAGCCUU---
.((((((((((......((....))....((((((((.....))))))))....)))))).))))(((..(((((((((.....)))))))))....)))..((((.....))))..--- ( -34.20)
>DroYak_CAF1 10053 117 + 1
AUAGAUCAAUUCAAACAGCACCAGCAGUCGGAGAAUGGAUUGCAUUUUUCUUUCGAUUAGCUCUGGCUGCAGUUGACUGAAUGUCAGUCGGCUCUUGAGCUUGGCUUUUAUAGCCUA---
................(((....((((((((((....(((((.(........))))))..))))))))))(((((((((.....))))))))).....))).((((.....))))..--- ( -38.80)
>DroAna_CAF1 9400 118 + 1
ACAGAUUAAUCCCAACAGCACCAAGAGACUGAUAUUUGCUUGCAUUU-UGUUUCUUUCAGCUUUCCGUGUAAUUGACUGAAGGU-GCUCGAUUGCAGAACCAGGCUUUUAUAGACACACU
.(((.(((((..((..(((...(((((((.((....((....)).))-.)))))))...))).....))..))))))))...((-(((.((..((........))..))..)).)))... ( -18.70)
>consensus
AUAGAUUAAUCCAAACAGCACCAGCAGUCGGAGAAUGGAUUGCAUUUUUCUUUCGAUUAGCUCUGGCUACAGUUGACUGAAUGUCAGUCGGCUCUUGAGCUUGGCUUUUAUAGCCUU___
.......................((((((........))))))...............(((((.((....(((((((((.....))))))))))).))))).((((.....))))..... (-23.08 = -23.76 +   0.68)

alignment

secondary structure

dotplot

Window 9

Location	13,142,860 – 13,142,968
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.19
Mean single sequence MFE	-31.59
Consensus MFE	-21.51
Energy contribution	-21.10
Covariance contribution	-0.41
Combinations/Pair	1.42
Mean z-score	-1.71
Structure conservation index	0.68
SVM decision value	0.58
SVM RNA-class probability	0.787834
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13142860 108 + 22407834
UGCAUUUUUCUUUCGAUUAGCUCUGGCUACAGUUGACUGAAUGUCAGUCGGCUCUUGAGCUGGGCUUUUAUAGCCUU------GCCCUGGGUUAUCAG------CAGUUCUAAGUGGUUG
........................(((((((((((((((.....)))))))))...((((((((((.....))))..------...((((....))))------))))))...)))))). ( -32.40)
>DroSec_CAF1 9931 111 + 1
UGCAUUUUUCUUUCGAUUAGCUCUGGCUACAGUUGACUGAAUGUCAGUCGGCUCUUGAGCUUGGCUUUUAUAGCCUU------GCCCUGGGUUAUCAGCA---GCAGUUCUAAGUGGUUG
.........(((..((((.(((((((..(((((((((((.....)))))))))((.(.((..((((.....))))..------)).).))))..)))).)---))))))..)))...... ( -32.40)
>DroSim_CAF1 10735 111 + 1
UGCAUUUUUCUUUCGAUUAGCUCUGGCUACAGUUGACUGAAUGUCAGUCGGCUCUUGAGCUUGGCUUUUAUAGCCUU------GCCCUGGGUUAUCAGCA---GCAGUUCUAAGUGGUUG
.........(((..((((.(((((((..(((((((((((.....)))))))))((.(.((..((((.....))))..------)).).))))..)))).)---))))))..)))...... ( -32.40)
>DroEre_CAF1 11850 104 + 1
----UUUUUCUUUCGAUUAGCUCAGGCUACAGUUGACUGAAUGUCAGUUGGUUCUUUAGCUUGGCUUUUAUAGCCUA------GCUCUGGGCUAUCAG------CAGUGUUAAAUGGCUG
----.............((((((((....((..((((.....))))..)).......((((.((((.....)))).)------))))))))))).(((------(.((.....)).)))) ( -32.90)
>DroYak_CAF1 10093 108 + 1
UGCAUUUUUCUUUCGAUUAGCUCUGGCUGCAGUUGACUGAAUGUCAGUCGGCUCUUGAGCUUGGCUUUUAUAGCCUA------GCCCUGGGUUAUCAG------CAGUUCUAAAUGAUUG
.............((((((.....(((((((((((((((.....)))))))))((.(.(((.((((.....)))).)------)).).)).......)------))))).....)))))) ( -33.50)
>DroAna_CAF1 9440 118 + 1
UGCAUUU-UGUUUCUUUCAGCUUUCCGUGUAAUUGACUGAAGGU-GCUCGAUUGCAGAACCAGGCUUUUAUAGACACACUCUGGGUCUGAGUUAUCAGCAAGUGCCAUUCUAUAUGUCUA
((((..(-((...((((((((.............).))))))).-...))).)))).....((((...((((((..((((....(.((((....))))).))))....)))))).)))). ( -25.92)
>consensus
UGCAUUUUUCUUUCGAUUAGCUCUGGCUACAGUUGACUGAAUGUCAGUCGGCUCUUGAGCUUGGCUUUUAUAGCCUU______GCCCUGGGUUAUCAG______CAGUUCUAAAUGGUUG
..............(((.(((((.(((...(((((((((.....))))))))).........((((.....))))........)))..))))))))........................ (-21.51 = -21.10 +  -0.41)

alignment

secondary structure

dotplot

Window 0

Location	13,142,860 – 13,142,968
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.19
Mean single sequence MFE	-29.24
Consensus MFE	-14.58
Energy contribution	-15.83
Covariance contribution	1.25
Combinations/Pair	1.21
Mean z-score	-2.94
Structure conservation index	0.50
SVM decision value	1.10
SVM RNA-class probability	0.915613
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13142860 108 - 22407834
CAACCACUUAGAACUG------CUGAUAACCCAGGGC------AAGGCUAUAAAAGCCCAGCUCAAGAGCCGACUGACAUUCAGUCAACUGUAGCCAGAGCUAAUCGAAAGAAAAAUGCA
.......((((..(((------(((........((((------..((((.....))))..)))).......(((((.....))))).....))).)))..))))((....))........ ( -28.50)
>DroSec_CAF1 9931 111 - 1
CAACCACUUAGAACUGC---UGCUGAUAACCCAGGGC------AAGGCUAUAAAAGCCAAGCUCAAGAGCCGACUGACAUUCAGUCAACUGUAGCCAGAGCUAAUCGAAAGAAAAAUGCA
.......((((..((((---(((.(........((((------..((((.....))))..)))).......(((((.....)))))..).)))).)))..))))((....))........ ( -31.60)
>DroSim_CAF1 10735 111 - 1
CAACCACUUAGAACUGC---UGCUGAUAACCCAGGGC------AAGGCUAUAAAAGCCAAGCUCAAGAGCCGACUGACAUUCAGUCAACUGUAGCCAGAGCUAAUCGAAAGAAAAAUGCA
.......((((..((((---(((.(........((((------..((((.....))))..)))).......(((((.....)))))..).)))).)))..))))((....))........ ( -31.60)
>DroEre_CAF1 11850 104 - 1
CAGCCAUUUAACACUG------CUGAUAGCCCAGAGC------UAGGCUAUAAAAGCCAAGCUAAAGAACCAACUGACAUUCAGUCAACUGUAGCCUGAGCUAAUCGAAAGAAAAA----
((((...........)------))).((((.(((.((------((((((.....))))............((..((((.....))))..))))))))).)))).((....))....---- ( -27.70)
>DroYak_CAF1 10093 108 - 1
CAAUCAUUUAGAACUG------CUGAUAACCCAGGGC------UAGGCUAUAAAAGCCAAGCUCAAGAGCCGACUGACAUUCAGUCAACUGCAGCCAGAGCUAAUCGAAAGAAAAAUGCA
.......((((..(((------(((........((((------(.((((.....)))).))))).......(((((.....))))).....))).)))..))))((....))........ ( -32.70)
>DroAna_CAF1 9440 118 - 1
UAGACAUAUAGAAUGGCACUUGCUGAUAACUCAGACCCAGAGUGUGUCUAUAAAAGCCUGGUUCUGCAAUCGAGC-ACCUUCAGUCAAUUACACGGAAAGCUGAAAGAAACA-AAAUGCA
......((((((...((((((.((((....)))).....)))))).))))))...((.((.((((((......))-...((((((..............)))))))))).))-....)). ( -23.34)
>consensus
CAACCACUUAGAACUG______CUGAUAACCCAGGGC______AAGGCUAUAAAAGCCAAGCUCAAGAGCCGACUGACAUUCAGUCAACUGUAGCCAGAGCUAAUCGAAAGAAAAAUGCA
.......((((...........(((......)))...........(((((((........(((....))).(((((.....)))))...)))))))....))))((....))........ (-14.58 = -15.83 +   1.25)

alignment

secondary structure

dotplot

Window 1

Location	13,142,900 – 13,143,008
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	73.14
Mean single sequence MFE	-21.81
Consensus MFE	-9.04
Energy contribution	-10.10
Covariance contribution	1.06
Combinations/Pair	1.08
Mean z-score	-1.88
Structure conservation index	0.41
SVM decision value	0.18
SVM RNA-class probability	0.619721
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13142900 108 - 22407834
CACUCACCUCUGUCUAAAAGUAUACAUAUCACCUUUAAACCAACCACUUAGAACUG------CUGAUAACCCAGGGC------AAGGCUAUAAAAGCCCAGCUCAAGAGCCGACUGACAU
((.((..((((...............(((((.(......................)------.))))).....((((------..((((.....))))..)))).))))..)).)).... ( -17.35)
>DroSec_CAF1 9971 111 - 1
CACUCACCUCAGUCUAAAAGUGUACAUAUCACCUUUAAACCAACCACUUAGAACUGC---UGCUGAUAACCCAGGGC------AAGGCUAUAAAAGCCAAGCUCAAGAGCCGACUGACAU
........((((((((((.(((.......))).)))).........(((.((.((((---(.(((......))))))------..((((.....)))).)).)))))....))))))... ( -23.50)
>DroSim_CAF1 10775 100 - 1
CACUCACCUCAGUCUAAAAGUGUA-----------UAAACCAACCACUUAGAACUGC---UGCUGAUAACCCAGGGC------AAGGCUAUAAAAGCCAAGCUCAAGAGCCGACUGACAU
........((((((...(((((..-----------.........))))).....(((---(.(((......))))))------).((((.....))))..(((....))).))))))... ( -23.30)
>DroEre_CAF1 11886 108 - 1
UACUCACCUCAAUCUAAGAGUAUGCAUAUAACCUUUAAACCAGCCAUUUAACACUG------CUGAUAGCCCAGAGC------UAGGCUAUAAAAGCCAAGCUAAAGAACCAACUGACAU
(((((............)))))..........(((((...((((...........)------)))..........((------(.((((.....)))).))))))))............. ( -18.00)
>DroYak_CAF1 10133 96 - 1
CACUCACCUCAGUCUAAAAGU------------CUUAAAGCAAUCAUUUAGAACUG------CUGAUAACCCAGGGC------UAGGCUAUAAAAGCCAAGCUCAAGAGCCGACUGACAU
........((((((.....(.------------.(((.((((.((.....))..))------))..)))..).((((------(.((((.....)))).))))).......))))))... ( -25.00)
>DroAna_CAF1 9479 113 - 1
CACUCACAUUAAUU----GGUAUAC-UACUACCUAUCUA-UAGACAUAUAGAAUGGCACUUGCUGAUAACUCAGACCCAGAGUGUGUCUAUAAAAGCCUGGUUCUGCAAUCGAGC-ACCU
..............----((((...-...))))....((-(((((((((....(((......((((....))))..)))..)))))))))))...((.(((((....))))).))-.... ( -23.70)
>consensus
CACUCACCUCAGUCUAAAAGUAUAC_UAU_ACCUUUAAACCAACCACUUAGAACUG______CUGAUAACCCAGGGC______AAGGCUAUAAAAGCCAAGCUCAAGAGCCGACUGACAU
........((((((................................................(((......)))...........((((.....)))).............))))))... ( -9.04 = -10.10 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:54 2006