Locus 5844

Sequence ID	2R_DroMel_CAF1
Location	18,497,309 – 18,497,660
Length	351
Max. P	0.972255

overview

Window 4

Location	18,497,309 – 18,497,423
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.01
Mean single sequence MFE	-29.34
Consensus MFE	-24.50
Energy contribution	-24.81
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-1.39
Structure conservation index	0.84
SVM decision value	-0.03
SVM RNA-class probability	0.516609
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18497309 114 - 20766785
GCUAAUUCAGACCUAGGCCAGCUAGGUUCAGCAGCCU---CCCAGCCU-UUCAG--CUGCUCUCCCCUCGCAUUACGUAUACGCCCCUUAUGCCACAUAUCACGUAUACGCAGUGCUUGA
.........(((((((.....))))))).((((((..---........-....)--)))))........(((((.((((((((.....((((...))))...)))))))).))))).... ( -31.44)
>DroSec_CAF1 15938 113 - 1
GCUAAUUCAGACCUAGGCCGUCUAGGUUCAGCAGCCU---CCCAGCCU-UUCAG--CGGCUCUCCCCUCGCAUUACGUAUACGCCCCU-CUGCCACAUAUCACGUAUACGCAGUGCUCGA
(((......(((((((.....)))))))....)))..---...((((.-.....--.))))........(((((.((((((((.....-.............)))))))).))))).... ( -28.27)
>DroSim_CAF1 5089 114 - 1
GCUAAUUCAGACCUAGGCCAGCUAGGUUCAGCAGCCUU--CCCAGCCA-UUCAG--CGGCUCUCCCCUCGCAUUACGUAUACGCCCCU-CUGCCACAUAUCACGUAUACGCAGUGCUCGA
(((......(((((((.....)))))))....)))...--...((((.-.....--.))))........(((((.((((((((.....-.............)))))))).))))).... ( -28.57)
>DroEre_CAF1 21505 119 - 1
GCUAAUUCAGGCCUAGACCAGCUAGGUUCAGCAGCCUUGCCUCAGCCGCUUCCGCCCAGCACUCCCCUCGCAUUACGUAUACGCCCCG-CUGCCACAUAUCACGUAUACGCAGUGCUUGA
(((......(((..((....((.((((......)))).))))..)))((....))..))).........(((((.((((((((.....-.............)))))))).))))).... ( -29.07)
>consensus
GCUAAUUCAGACCUAGGCCAGCUAGGUUCAGCAGCCU___CCCAGCCU_UUCAG__CGGCUCUCCCCUCGCAUUACGUAUACGCCCCU_CUGCCACAUAUCACGUAUACGCAGUGCUCGA
(((......(((((((.....)))))))....))).........(((..........))).........(((((.((((((((...................)))))))).))))).... (-24.50 = -24.81 +   0.31)

alignment

secondary structure

dotplot

Window 5

Location	18,497,386 – 18,497,500
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.78
Mean single sequence MFE	-33.20
Consensus MFE	-22.33
Energy contribution	-22.57
Covariance contribution	0.25
Combinations/Pair	1.04
Mean z-score	-1.72
Structure conservation index	0.67
SVM decision value	0.07
SVM RNA-class probability	0.570194
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18497386 114 + 20766785
---AGGCUGCUGAACCUAGCUGGCCUAGGUCUGAAUUAGCAUAAUAUGCCAAAAUGGCAGUUUUUUAAGAAUUCGCCAUAAGUGU---UGGGUUUCUCAACCAAAAAGUGCCAGCCUUUG
---(((((((((....)))).(((((.(((..(((((.........((((.....))))..........))))))))....(.((---((((...)))))))....)).))))))))... ( -31.21)
>DroSec_CAF1 16014 115 + 1
---AGGCUGCUGAACCUAGACGGCCUAGGUCUGAAUUAGCAUAAUAUGCCAUAAUGGCAGUUUUUUAACAAUUCGCCAUAAGUGUUGUUGGGUUUCUAAGCCAAAA--GGACUGCCUUUG
---.(((((((((((((((.....)))))).....))))))......))).....(((((((((((..((((.(((.....)))..))))((((....)))).)))--)))))))).... ( -36.20)
>DroSim_CAF1 5165 116 + 1
--AAGGCUGCUGAACCUAGCUGGCCUAGGUCUGAAUUAGCAUAAUAUGCCAUAAUGGCAGUUUUUUAACAAUUCGCCAUAAGUGUUGUUGGGUUUCUAAGCCAAAG--GGCCUGCCUUUG
--..((((...(((((((((.(((((.(((..(((((.........((((.....))))(((....)))))))))))...)).))))))))))))...)))).(((--((....))))). ( -34.80)
>DroEre_CAF1 21584 114 + 1
GCAAGGCUGCUGAACCUAGCUGGUCUAGGCCUGAAUUAGCAUAAUAUGCCAUAAUGGCAGUUUUUUAACAAUAC-CCAUAAGUGU---UGGAUUUGAAAACCGAAG--GGUCUGCCUUUG
((.(((((((((....)))).)))))((((((..............((((.....))))((((((...((((((-......))))---)).....))))))....)--)))))))..... ( -30.60)
>consensus
___AGGCUGCUGAACCUAGCUGGCCUAGGUCUGAAUUAGCAUAAUAUGCCAUAAUGGCAGUUUUUUAACAAUUCGCCAUAAGUGU___UGGGUUUCUAAACCAAAA__GGCCUGCCUUUG
...((((((((((((((((.....)))))).....)))))).....((((.....))))...............................((((....))))...........))))... (-22.33 = -22.57 +   0.25)

alignment

secondary structure

dotplot

Window 6

Location	18,497,386 – 18,497,500
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.78
Mean single sequence MFE	-30.16
Consensus MFE	-22.16
Energy contribution	-22.97
Covariance contribution	0.81
Combinations/Pair	1.07
Mean z-score	-1.93
Structure conservation index	0.73
SVM decision value	0.56
SVM RNA-class probability	0.783299
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18497386 114 - 20766785
CAAAGGCUGGCACUUUUUGGUUGAGAAACCCA---ACACUUAUGGCGAAUUCUUAAAAAACUGCCAUUUUGGCAUAUUAUGCUAAUUCAGACCUAGGCCAGCUAGGUUCAGCAGCCU---
....(((((((.((....((((..(((.....---......((((((..............)))))).(((((((...)))))))))).)))).)))))))))((((......))))--- ( -32.44)
>DroSec_CAF1 16014 115 - 1
CAAAGGCAGUCC--UUUUGGCUUAGAAACCCAACAACACUUAUGGCGAAUUGUUAAAAAACUGCCAUUAUGGCAUAUUAUGCUAAUUCAGACCUAGGCCGUCUAGGUUCAGCAGCCU---
...((((.((((--(..((((((((................((((((..((......))..))))))..((((((...))))))........))))))))...)))....)).))))--- ( -29.50)
>DroSim_CAF1 5165 116 - 1
CAAAGGCAGGCC--CUUUGGCUUAGAAACCCAACAACACUUAUGGCGAAUUGUUAAAAAACUGCCAUUAUGGCAUAUUAUGCUAAUUCAGACCUAGGCCAGCUAGGUUCAGCAGCCUU--
..(((((.(..(--(((((((((((................((((((..((......))..))))))..((((((...))))))........)))))))))..)))..)....)))))-- ( -31.10)
>DroEre_CAF1 21584 114 - 1
CAAAGGCAGACC--CUUCGGUUUUCAAAUCCA---ACACUUAUGG-GUAUUGUUAAAAAACUGCCAUUAUGGCAUAUUAUGCUAAUUCAGGCCUAGACCAGCUAGGUUCAGCAGCCUUGC
....((((((((--....)))...((((((((---.......)))-)).)))........)))))....((((((...))))))....((((((..(((.....)))..))..))))... ( -27.60)
>consensus
CAAAGGCAGGCC__CUUUGGCUUAGAAACCCA___ACACUUAUGGCGAAUUGUUAAAAAACUGCCAUUAUGGCAUAUUAUGCUAAUUCAGACCUAGGCCAGCUAGGUUCAGCAGCCU___
...((((...........(((((((................((((((..((......))..))))))..((((((...))))))........))))))).(((......))).))))... (-22.16 = -22.97 +   0.81)

alignment

secondary structure

dotplot

Window 7

Location	18,497,463 – 18,497,580
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.31
Mean single sequence MFE	-21.18
Consensus MFE	-15.99
Energy contribution	-16.05
Covariance contribution	0.06
Combinations/Pair	1.12
Mean z-score	-1.64
Structure conservation index	0.76
SVM decision value	0.21
SVM RNA-class probability	0.635703
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18497463 117 - 20766785
GAACAGAUCCAUUCAGUCUGGCCAAAAAGUUAUUAAAUUAUUUUAAAAUCAAACCAUCCAUCCAUUGCACUGCGCAGCCACAAAGGCUGGCACUUUUUGGUUGAGAAACCCA---ACACU
...(((((.......)))))((((((((((..(((((....))))).........................((.(((((.....)))))))))))))))))...........---..... ( -26.70)
>DroSec_CAF1 16091 118 - 1
GAACAGACCCAUUCUGUCUGGCCAAAAAGUUAUUAAAUUAUUUUAAGAUCAAACCAUCCAUCCAUUGCACUGCGCAGCCACAAAGGCAGUCC--UUUUGGCUUAGAAACCCAACAACACU
...(((((.......)))))(((((((.....(((((....)))))(((................(((.....)))(((.....))).))).--)))))))................... ( -20.60)
>DroSim_CAF1 5243 118 - 1
GAACAGACCCAUUCUGUCUGGCCAAAAAGUUAUUAAAUUAUUUUAAAAUCAAACCAUCCAUCCAUUGCACUGCGCAGCCACAAAGGCAGGCC--CUUUGGCUUAGAAACCCAACAACACU
...(((((.......)))))((((((......(((((....))))).......((..........(((.....)))(((.....))).))..--.))))))................... ( -21.10)
>DroEre_CAF1 21663 112 - 1
GAACAGACCCAUUUUGUCUGGCCAAAAAGUUAUUAAAUUAUUUUAAAAUCAAACCAUCCAU---UUGCACUGCACAGCCACAAAGGCAGACC--CUUCGGUUUUCAAAUCCA---ACACU
(..(((((.......)))))..).....(((.(((((....)))))....(((((......---.(((...)))..(((.....))).....--....)))))........)---))... ( -16.30)
>consensus
GAACAGACCCAUUCUGUCUGGCCAAAAAGUUAUUAAAUUAUUUUAAAAUCAAACCAUCCAUCCAUUGCACUGCGCAGCCACAAAGGCAGGCC__CUUUGGCUUAGAAACCCA___ACACU
...(((((.......)))))((((((.......................................(((.....)))(((.....)))........))))))................... (-15.99 = -16.05 +   0.06)

alignment

secondary structure

dotplot

Window 8

Location	18,497,540 – 18,497,660
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.11
Mean single sequence MFE	-37.05
Consensus MFE	-35.42
Energy contribution	-35.17
Covariance contribution	-0.25
Combinations/Pair	1.11
Mean z-score	-2.37
Structure conservation index	0.96
SVM decision value	1.69
SVM RNA-class probability	0.972255
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18497540 120 + 20766785
UAAUUUAAUAACUUUUUGGCCAGACUGAAUGGAUCUGUUCAAUGCAGGCGGGCCGAAGAAGGGAUUGACAAGGCGGAAAACAUUUUGCCUGGCAAGGCCUAAAACACGCUUGAAUUAUUC
((((((((....(((((((((...(((..((((....))))...)))...)))))))))(((..(((...((((((((....))))))))..)))..))).........))))))))... ( -36.60)
>DroSec_CAF1 16169 120 + 1
UAAUUUAAUAACUUUUUGGCCAGACAGAAUGGGUCUGUUCAAGGCAGGCGGGCCGAAGAAGGGAUUGACAAGGCGGAAAACAUUUUGCCUGGCAAGGCCUAAAACACGCUUGAAUUAUUC
((((((((....(((((((((...(.....).((((((.....)))))).)))))))))(((..(((...((((((((....))))))))..)))..))).........))))))))... ( -36.70)
>DroSim_CAF1 5321 120 + 1
UAAUUUAAUAACUUUUUGGCCAGACAGAAUGGGUCUGUUCAAGGCAGGCGGGCCAAAGAAGGGAUUGACAAGGCGGAAAACAUUUUGCCUGGCAAGGCCUAAAACACGCUUGAAUUAUUC
((((((((....(((((((((...(.....).((((((.....)))))).)))))))))(((..(((...((((((((....))))))))..)))..))).........))))))))... ( -37.00)
>DroEre_CAF1 21735 120 + 1
UAAUUUAAUAACUUUUUGGCCAGACAAAAUGGGUCUGUUCAAUGCAGGCGGGCCGAGAAGGGGAUUGACAAGGCGGAAAACAUUUUGCCCGGCAAGGCCUAAAACACGCUUGAAUUAUUC
((((((((...((((((((((...(.....).((((((.....)))))).))))))))))(((.(((.(..(((((((....)))))))..))))..))).........))))))))... ( -37.90)
>consensus
UAAUUUAAUAACUUUUUGGCCAGACAGAAUGGGUCUGUUCAAGGCAGGCGGGCCGAAGAAGGGAUUGACAAGGCGGAAAACAUUUUGCCUGGCAAGGCCUAAAACACGCUUGAAUUAUUC
((((((((....(((((((((...(.....).((((((.....)))))).)))))))))(((..(((...((((((((....))))))))..)))..))).........))))))))... (-35.42 = -35.17 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:08 2006