Locus 5653

Sequence ID	X_DroMel_CAF1
Location	14,605,296 – 14,605,528
Length	232
Max. P	0.877547

overview

Window 3

Location	14,605,296 – 14,605,411
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.10
Mean single sequence MFE	-25.24
Consensus MFE	-18.92
Energy contribution	-19.00
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.55
Structure conservation index	0.75
SVM decision value	0.00
SVM RNA-class probability	0.533847
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14605296 115 + 22224390
AACUUGGGGCCAUGGAAGACAAUAAAUAUUUAUAUGUAAAUGCCGGCAAUAUUGUCU-CUAUU-GUGCACAC-AGGGCACCAAACAAACAAAAAAAAAAGAAGAAGGUGGG-GAU-CCUG
...((((.(((.((((.(((((((.((((....))))...((....)).))))))))-)))((-((....))-))))).)))).....................(((....-...-))). ( -21.60)
>DroSec_CAF1 79761 118 + 1
AACUUGGGGCCAUGGAAGACAAUAAAUAUUUAUAUGUAAAUGCCAGCAAUAUUGUCUUCUAUUGGUGCACACCAGGGCACCAAACAAACAAAUAAGGA--AAAAAGGUGGGGGAUCCCAG
....(((((((.((((((((((((.((((....))))...((....)).))))))))))))(((((((........)))))))...............--...........)).))))). ( -33.80)
>DroSim_CAF1 79826 112 + 1
AACUUGGGGCCAUGGAAGACAAUAAAUAUUUAUAUGUAAAUGCCAGCAAUAUUGUCU-CUAUU-GUGCACAC-AGGGCACCAAACAAACAAACAAA-A--AAAAAGGUGGG-GAU-CCAG
...((((.(((.((((.(((((((.((((....))))...((....)).))))))))-)))((-((....))-))))).)))).............-.--.......(((.-...-))). ( -21.60)
>DroEre_CAF1 74631 93 + 1
AACUUGGGGCCAUGGAAGACAAUAAAUAUUUAUAUGUAAAUGCCGGCAAUAUUGUCU-CUAUU-GUG-GCAC-AGGGCACCA---------------------AAGGUGGG-CAU-UCUG
..((((..((((..(.((((((((.((((....))))...((....)).))))))))-...).-.))-)).)-)))((.(((---------------------....))))-)..-.... ( -24.90)
>DroYak_CAF1 75979 111 + 1
AACUUGGGGCCAUGGAAGACAAUAAAUAUUUAUAUGUAAAUGCCGGCAAUAUUGUCU-UCAUU-GUGCACAC-AGGGCACCAAACAAACAAACGCA----AAAAAGGUGGA-GAU-UUUG
...((((.(((...((((((((((.((((....))))...((....)).))))))))-)).((-((....))-))))).)))).((((....(((.----......)))..-...-)))) ( -24.30)
>consensus
AACUUGGGGCCAUGGAAGACAAUAAAUAUUUAUAUGUAAAUGCCGGCAAUAUUGUCU_CUAUU_GUGCACAC_AGGGCACCAAACAAACAAACAAA_A__AAAAAGGUGGG_GAU_CCUG
...((((.(((.(((.((((((((.((((....))))...((....)).)))))))).)))(((((....)))))))).))))..................................... (-18.92 = -19.00 +   0.08)

alignment

secondary structure

dotplot

Window 4

Location	14,605,373 – 14,605,489
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.10
Mean single sequence MFE	-28.72
Consensus MFE	-21.92
Energy contribution	-22.76
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-1.52
Structure conservation index	0.76
SVM decision value	0.02
SVM RNA-class probability	0.541739
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14605373 116 + 22224390
CAAACAAACAAAAAAAAAAGAAGAAGGUGGG-GAU-CCUGCUAACCUGAGUC-CGGAGGGUACAGUUCACACCAUGCUAAGUGCGCCGG-AGGUCGCACUAAAGUAAGCCAUUAAAUGUA
.......(((...............((((.(-(((-..((((..((......-.))..))))..)))).)))).((((.((((((((..-.)).))))))..))))..........))). ( -27.10)
>DroSec_CAF1 79841 118 + 1
CAAACAAACAAAUAAGGA--AAAAAGGUGGGGGAUCCCAGCUAACCUGAGCCCCGGAGGGUACAGUUCACACCCUGCUAAGUGCGCCGGAAGGUCGCACUAAAGUAAGCCAUUAAAUGUA
.......(((..(((((.--.....(((((((...))).......(((.((((....)))).)))....)))).((((.((((((((....)).))))))..))))..)).)))..))). ( -36.20)
>DroSim_CAF1 79903 113 + 1
CAAACAAACAAACAAA-A--AAAAAGGUGGG-GAU-CCAGCUAACCUGAGCC-CGGAGGGUACAGUUUACACCAUGCUAAGUGCGCCGG-AGGUCGCACUAAAGUAAGCCAUUAAAUGUA
...........(((..-.--.....((((((-...-))...(((.(((.(((-(...)))).))).))))))).((((.((((((((..-.)).))))))..))))..........))). ( -26.20)
>DroEre_CAF1 74707 95 + 1
CA---------------------AAGGUGGG-CAU-UCUGCUGACCUGAACC-CGCAGGGCACAGUUCACACCAUGCUAAGUGCACCGG-AGGUCGCACUAAAGUAAGCCAUUAAGUGUA
..---------------------..(((.((-(((-..((.(((.(((..((-(...)))..))).)))))..))))).((((((((..-.))).))))).......))).......... ( -26.60)
>DroYak_CAF1 76056 112 + 1
CAAACAAACAAACGCA----AAAAAGGUGGA-GAU-UUUGCUAACCUAAACC-CGGAGGGUACAGUUCACACCAUGCUAAGUGCGCCAG-AGGUCGCACUAAAGUAAGACAUUAAAUGUA
.............(((----.....((((..-(((-(.((((..((......-.))..)))).))))..)))).((((.((((((((..-.)).))))))..))))..........))). ( -27.50)
>consensus
CAAACAAACAAACAAA_A__AAAAAGGUGGG_GAU_CCUGCUAACCUGAGCC_CGGAGGGUACAGUUCACACCAUGCUAAGUGCGCCGG_AGGUCGCACUAAAGUAAGCCAUUAAAUGUA
.........................((((...(((...((((..((........))..))))..)))..)))).((((.((((((((....)).))))))..)))).............. (-21.92 = -22.76 +   0.84)

alignment

secondary structure

dotplot

Window 5

Location	14,605,411 – 14,605,528
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.26
Mean single sequence MFE	-37.14
Consensus MFE	-26.24
Energy contribution	-27.84
Covariance contribution	1.60
Combinations/Pair	1.14
Mean z-score	-2.39
Structure conservation index	0.71
SVM decision value	0.47
SVM RNA-class probability	0.749828
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14605411 117 + 22224390
CUAACCUGAGUC-CGGAGGGUACAGUUCACACCAUGCUAAGUGCGCCGG-AGGUCGCACUAAAGUAAGCCAUUAAAUGUAACAAU-UGAUAUAAUUGUACGCAUUAUUUGGGCUGCAGGA
....((((((((-((((((.((((((.........))).((((((((..-.)).))))))...)))..))....(((((.(((((-((...)))))))..))))).)))))))).)))). ( -35.50)
>DroSec_CAF1 79879 120 + 1
CUAACCUGAGCCCCGGAGGGUACAGUUCACACCCUGCUAAGUGCGCCGGAAGGUCGCACUAAAGUAAGCCAUUAAAUGUAACAAUUUGAUAUAAUUGUACCCAUUGCUUUGGCUGCAGGA
....((((((((..((.((((((((((.......((((.((((((((....)).))))))..))))....(((((((......)))))))..))))))))))....))..)))).)))). ( -46.40)
>DroSim_CAF1 79938 117 + 1
CUAACCUGAGCC-CGGAGGGUACAGUUUACACCAUGCUAAGUGCGCCGG-AGGUCGCACUAAAGUAAGCCAUUAAAUGUAACAAU-UGAUAUAAUUGUACCCAUUGCUUGGGCUGCAGGA
....((((((((-(((.((((((((((.......((((.((((((((..-.)).))))))..))))....(((((.((...)).)-))))..))))))))))....).)))))).)))). ( -41.00)
>DroEre_CAF1 74724 116 + 1
CUGACCUGAACC-CGCAGGGCACAGUUCACACCAUGCUAAGUGCACCGG-AGGUCGCACUAAAGUAAGCCAUUAAGUGUAACAAU-UGACAUAAUUGUAUCCAUUGCGUGUGCUGCGGA-
...........(-(((((.((((...........((((.((((((((..-.))).)))))..)))).((.....((((..(((((-((...)))))))...)))))))))).)))))).- ( -34.00)
>DroYak_CAF1 76090 116 + 1
CUAACCUAAACC-CGGAGGGUACAGUUCACACCAUGCUAAGUGCGCCAG-AGGUCGCACUAAAGUAAGACAUUAAAUGUAACAAU-UGAUAUAAUUGUACCCAUUGCGUGUGCUGCAGC-
....((......-.)).((((((((((.......((((.((((((((..-.)).))))))..))))..((((...))))......-......)))))))))).(((((.....))))).- ( -28.80)
>consensus
CUAACCUGAGCC_CGGAGGGUACAGUUCACACCAUGCUAAGUGCGCCGG_AGGUCGCACUAAAGUAAGCCAUUAAAUGUAACAAU_UGAUAUAAUUGUACCCAUUGCUUGGGCUGCAGGA
....((((((((.(((.((((((((((.......((((.((((((((....)).))))))..)))).........((((.........)))))))))))))).)))....)))).)))). (-26.24 = -27.84 +   1.60)

alignment

secondary structure

dotplot

Window 6

Location	14,605,411 – 14,605,528
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.26
Mean single sequence MFE	-35.72
Consensus MFE	-28.60
Energy contribution	-29.04
Covariance contribution	0.44
Combinations/Pair	1.18
Mean z-score	-1.81
Structure conservation index	0.80
SVM decision value	0.90
SVM RNA-class probability	0.877547
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14605411 117 - 22224390
UCCUGCAGCCCAAAUAAUGCGUACAAUUAUAUCA-AUUGUUACAUUUAAUGGCUUACUUUAGUGCGACCU-CCGGCGCACUUAGCAUGGUGUGAACUGUACCCUCCG-GACUCAGGUUAG
.((((.((.((.....((((((((((((.....)-)))).))).................((((((.((.-..))))))))..))))((.(((.....)))))...)-).)))))).... ( -28.30)
>DroSec_CAF1 79879 120 - 1
UCCUGCAGCCAAAGCAAUGGGUACAAUUAUAUCAAAUUGUUACAUUUAAUGGCUUACUUUAGUGCGACCUUCCGGCGCACUUAGCAGGGUGUGAACUGUACCCUCCGGGGCUCAGGUUAG
(((((((((((....((((...((((((......))))))..))))...)))))......((((((.((....))))))))..))))))......(((..(((....)))..)))..... ( -41.00)
>DroSim_CAF1 79938 117 - 1
UCCUGCAGCCCAAGCAAUGGGUACAAUUAUAUCA-AUUGUUACAUUUAAUGGCUUACUUUAGUGCGACCU-CCGGCGCACUUAGCAUGGUGUAAACUGUACCCUCCG-GGCUCAGGUUAG
.((((.(((((.......(((((((.((((((((-.......(((...)))(((......((((((.((.-..)))))))).))).))))))))..)))))))...)-)))))))).... ( -42.10)
>DroEre_CAF1 74724 116 - 1
-UCCGCAGCACACGCAAUGGAUACAAUUAUGUCA-AUUGUUACACUUAAUGGCUUACUUUAGUGCGACCU-CCGGUGCACUUAGCAUGGUGUGAACUGUGCCCUGCG-GGUUCAGGUCAG
-(((((((..((((((((.((((......)))).-)))))((((((.....(((......(((((.(((.-..)))))))).)))..))))))....)))..)))))-)).......... ( -36.40)
>DroYak_CAF1 76090 116 - 1
-GCUGCAGCACACGCAAUGGGUACAAUUAUAUCA-AUUGUUACAUUUAAUGUCUUACUUUAGUGCGACCU-CUGGCGCACUUAGCAUGGUGUGAACUGUACCCUCCG-GGUUUAGGUUAG
-.(((.(((...((....(((((((.((((((((-..((((((((...))).........((((((.((.-..)))))))))))))))))))))..)))))))..))-.))))))..... ( -30.80)
>consensus
UCCUGCAGCCCAAGCAAUGGGUACAAUUAUAUCA_AUUGUUACAUUUAAUGGCUUACUUUAGUGCGACCU_CCGGCGCACUUAGCAUGGUGUGAACUGUACCCUCCG_GGCUCAGGUUAG
.((((.((((........(((((((.((((((((...(((((((.....)).........((((((.((....)))))))))))))))))))))..))))))).....)))))))).... (-28.60 = -29.04 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:18 2006