Locus 6137

Sequence ID	2L_DroMel_CAF1
Location	17,133,854 – 17,134,208
Length	354
Max. P	0.999201

overview

Window 3

Location	17,133,854 – 17,133,972
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.97
Mean single sequence MFE	-33.06
Consensus MFE	-28.09
Energy contribution	-28.01
Covariance contribution	-0.08
Combinations/Pair	1.12
Mean z-score	-2.94
Structure conservation index	0.85
SVM decision value	3.43
SVM RNA-class probability	0.999201
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17133854 118 + 22407834
ACCUCUGUCUUCUCAAUUUUCCACCCAACUGAUGGGGAACGUGUAAAGGUUUAAAGUGUGGGCAACUGGAGGGA-AAAAGU-AGACAGAAAAACGGAAAAGCGCAAACAUUGCGCAGCAA
...(((((((.((...((((((..((.(((......((((.(....).))))..)))..((....))))..)))-))))).-)))))))...........(((((.....)))))..... ( -32.50)
>DroSec_CAF1 102321 118 + 1
ACCUCUGUCUUCUCAAUUUUCCACCCAUCUUAUGGGGCACGUGCAAAGGUUCAAAGUGUAGGCAACUGGAGGAA-AAAUGU-AGACAGAAAAACAGAAAAGCGCAAACAUUGCGCAGCAA
...(((((((...((.((((((.(((((...)))))((((..((....)).....))))((....))...))))-)).)).-)))))))...........(((((.....)))))..... ( -35.60)
>DroSim_CAF1 114510 112 + 1
ACCUCUGUCUUCUCAAUUUUCCACCCAUCUUAUGGGGCACGUGCAAAGGUUCAAAGUGU-------UGGAGGAAAAAAAGU-AGACAGAAAAACAGAAAAGCGCAAACAUUGCGCAGCAA
...(((((((.((...((((((.(((((...)))))((((..((....)).....))))-------....))))))..)).-)))))))...........(((((.....)))))..... ( -32.50)
>DroEre_CAF1 99883 119 + 1
ACCUCUGUCUUCUUAAUUUUCCACCCAUCACUUGGGGCACGUGCAGAUGCUCAAAGUGUAGGCAACUGAAGGAA-CAAAAUAAGACAGAAAAACAGAGAAGCGCAAACAUUGCGCAGCAA
...((((((((.......((((......(((((.((((((.....).))))).)))))(((....)))..))))-......))))))))...........(((((.....)))))..... ( -35.62)
>DroYak_CAF1 102227 118 + 1
ACCUCUGUCUUCUCAAUUUUCCACCCAUCACUUGGGGCACGUGCAAAGGUUCAAAGUGUAGGCAACUGAAGAAA-AAAAAC-AGACAGAAAAACAGAAAAGCGCAAACAUUGCGCAGCAA
...(((((((......(((((..((((.....))))((((..((....)).....))))((....))...))))-).....-)))))))...........(((((.....)))))..... ( -29.10)
>consensus
ACCUCUGUCUUCUCAAUUUUCCACCCAUCUCAUGGGGCACGUGCAAAGGUUCAAAGUGUAGGCAACUGGAGGAA_AAAAGU_AGACAGAAAAACAGAAAAGCGCAAACAUUGCGCAGCAA
...(((((((........((((.((((.....))))((((..((....)).....))))...........))))........)))))))...........(((((.....)))))..... (-28.09 = -28.01 +  -0.08)

alignment

secondary structure

dotplot

Window 4

Location	17,133,933 – 17,134,052
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.82
Mean single sequence MFE	-26.44
Consensus MFE	-26.60
Energy contribution	-26.36
Covariance contribution	-0.24
Combinations/Pair	1.03
Mean z-score	-1.58
Structure conservation index	1.01
SVM decision value	1.91
SVM RNA-class probability	0.982346
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17133933 119 + 22407834
U-AGACAGAAAAACGGAAAAGCGCAAACAUUGCGCAGCAAACAAAGUCAGUGGCCAUUUGCUUGUUCUGCUCCCAACUCCUGGCUCCUAAUGGCCAAAAUAUUGUAUUACAACAAAUUGU
.-..((((......(((...(((((.....)))))(((((((((.((.(((....))).))))))).))))......)))(((((......))))).....))))............... ( -25.70)
>DroSec_CAF1 102400 119 + 1
U-AGACAGAAAAACAGAAAAGCGCAAACAUUGCGCAGCAAACAAAGUCAGUGGCCAUUUGCUUGUUCUGCUCCCAACUCCUGGCUCCUAAUGGCCAAAAUAUUGUAUUACAACAAAUUGU
.-..((((............(((((.....))))).....((((.((...((((((((.(((.(((........)))....)))....))))))))..)).))))...........)))) ( -25.60)
>DroSim_CAF1 114583 119 + 1
U-AGACAGAAAAACAGAAAAGCGCAAACAUUGCGCAGCAAACAAAGUCAGUGGCCAUUUGCUUGUUCUGCUCCCAACUCCUGGCUCCUAAUGGCCAAAAUAUUGUAUUACAACAAAUUGU
.-..((((............(((((.....))))).....((((.((...((((((((.(((.(((........)))....)))....))))))))..)).))))...........)))) ( -25.60)
>DroEre_CAF1 99962 120 + 1
UAAGACAGAAAAACAGAGAAGCGCAAACAUUGCGCAGCAAACAAAGUCAGUGGCCAUUUGCCUGUUUUGCUCCCAACUCCUGGCUCCUAAUGGCCAAAAUAUUGUAUUACAACAAAUUGU
....((((............(((((.....))))).....((((.((...((((((((.(((.(..(((....)))..)..)))....))))))))..)).))))...........)))) ( -27.80)
>DroYak_CAF1 102306 119 + 1
C-AGACAGAAAAACAGAAAAGCGCAAACAUUGCGCAGCAAACAAAGUCAGUGGCCAUUUGCCUGUUCUGCUCCCAACUCCUGGCUCCUAAUGGCCAAAAUAUUGUAUUACAACAAAUUGU
.-..((((............(((((.....))))).....((((.((...((((((((.(((.(((........)))....)))....))))))))..)).))))...........)))) ( -27.50)
>consensus
U_AGACAGAAAAACAGAAAAGCGCAAACAUUGCGCAGCAAACAAAGUCAGUGGCCAUUUGCUUGUUCUGCUCCCAACUCCUGGCUCCUAAUGGCCAAAAUAUUGUAUUACAACAAAUUGU
....((((............(((((.....))))).....((((.((...((((((((.(((.(((........)))....)))....))))))))..)).))))...........)))) (-26.60 = -26.36 +  -0.24)

alignment

secondary structure

dotplot

Window 5

Location	17,134,012 – 17,134,131
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.31
Mean single sequence MFE	-26.95
Consensus MFE	-21.25
Energy contribution	-22.85
Covariance contribution	1.60
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.79
SVM decision value	0.08
SVM RNA-class probability	0.573233
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17134012 119 + 22407834
UGGCUCCUAAUGGCCAAAAUAUUGUAUUACAACAAAUUGUGCAUCUGGCCCGUAAAUAAA-AAGAGCAAGCCAAAACGGGCCGAAAACACCCUUUAAAACGGACCUCGAAACGGUCCUUG
(((((......))))).....((((......))))...(((....((((((((.......-..............))))))))....)))..........(((((.......)))))... ( -29.50)
>DroSec_CAF1 102479 119 + 1
UGGCUCCUAAUGGCCAAAAUAUUGUAUUACAACAAAUUGUGCAUCUGGCCCGUAAAUAAA-AAGAGCAAGCCAAAACGGGCCGAGAACACCCUUUAAAACGGACCUCGAAACGGUCCUUG
(((((......))))).....((((......))))...(((..((((((((((.......-..............))))))).))).)))..........(((((.......)))))... ( -31.00)
>DroSim_CAF1 114662 114 + 1
UGGCUCCUAAUGGCCAAAAUAUUGUAUUACAACAAAUUGUGCAUCUGGCCCGUAAAUAAA-AAGAGCAAGCCAAAACGGGCCGAGAACACCCUUUAAAACGGACCUC-----GGUCCUUG
(((((......))))).....((((......))))...(((..((((((((((.......-..............))))))).))).)))..........((((...-----.))))... ( -29.50)
>DroEre_CAF1 100042 119 + 1
UGGCUCCUAAUGGCCAAAAUAUUGUAUUACAACAAAUUGUGCAUCUGGCCCGUAAAUAAAAAAGAGAAGGCCAAAAC-AGCAGAAAACACCCUUUAAAACGGACCUCGAAACGGUCCUUG
(((((......))))).....((((......)))).((.(((...(((((..................)))))....-.))).))...............(((((.......)))))... ( -24.27)
>DroYak_CAF1 102385 117 + 1
UGGCUCCUAAUGGCCAAAAUAUUGUAUUACAACAAAUUGUGCAUCUGGCCCGUAAAUAAAAAAGAGCUGGCCAAACA-GGCAGA--ACACCCUUUAAAACGAACCUCGAAACGGUCCUUG
(((((......)))))......(((((...........)))))...((.((((..........(..(((.((.....-))))).--.)...........((.....))..)))).))... ( -20.50)
>consensus
UGGCUCCUAAUGGCCAAAAUAUUGUAUUACAACAAAUUGUGCAUCUGGCCCGUAAAUAAA_AAGAGCAAGCCAAAACGGGCCGAAAACACCCUUUAAAACGGACCUCGAAACGGUCCUUG
(((((......))))).....((((......))))...(((....((((((((......................))))))))....)))..........(((((.......)))))... (-21.25 = -22.85 +   1.60)

alignment

secondary structure

dotplot

Window 6

Location	17,134,012 – 17,134,131
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.31
Mean single sequence MFE	-35.76
Consensus MFE	-31.04
Energy contribution	-31.04
Covariance contribution	-0.00
Combinations/Pair	1.06
Mean z-score	-2.14
Structure conservation index	0.87
SVM decision value	2.58
SVM RNA-class probability	0.995502
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17134012 119 - 22407834
CAAGGACCGUUUCGAGGUCCGUUUUAAAGGGUGUUUUCGGCCCGUUUUGGCUUGCUCUU-UUUAUUUACGGGCCAGAUGCACAAUUUGUUGUAAUACAAUAUUUUGGCCAUUAGGAGCCA
........(((((..(((((((..(((((((.((....((((......)))).)).)))-))))...))))))).((((..(((..(((((.....)))))..)))..)))).))))).. ( -37.30)
>DroSec_CAF1 102479 119 - 1
CAAGGACCGUUUCGAGGUCCGUUUUAAAGGGUGUUCUCGGCCCGUUUUGGCUUGCUCUU-UUUAUUUACGGGCCAGAUGCACAAUUUGUUGUAAUACAAUAUUUUGGCCAUUAGGAGCCA
........(((((..(((((((..(((((((.((....((((......)))).)).)))-))))...))))))).((((..(((..(((((.....)))))..)))..)))).))))).. ( -37.30)
>DroSim_CAF1 114662 114 - 1
CAAGGACC-----GAGGUCCGUUUUAAAGGGUGUUCUCGGCCCGUUUUGGCUUGCUCUU-UUUAUUUACGGGCCAGAUGCACAAUUUGUUGUAAUACAAUAUUUUGGCCAUUAGGAGCCA
...((.((-----..(((((((..(((((((.((....((((......)))).)).)))-))))...))))))).((((..(((..(((((.....)))))..)))..)))).))..)). ( -37.20)
>DroEre_CAF1 100042 119 - 1
CAAGGACCGUUUCGAGGUCCGUUUUAAAGGGUGUUUUCUGCU-GUUUUGGCCUUCUCUUUUUUAUUUACGGGCCAGAUGCACAAUUUGUUGUAAUACAAUAUUUUGGCCAUUAGGAGCCA
...(((((.......)))))((((..((.(((......(((.-..((((((((................)))))))).)))(((..(((((.....)))))..)))))).))..)))).. ( -34.19)
>DroYak_CAF1 102385 117 - 1
CAAGGACCGUUUCGAGGUUCGUUUUAAAGGGUGU--UCUGCC-UGUUUGGCCAGCUCUUUUUUAUUUACGGGCCAGAUGCACAAUUUGUUGUAAUACAAUAUUUUGGCCAUUAGGAGCCA
........(((((..(((((((...(((((((..--...(((-.....)))..))))))).......))))))).((((..(((..(((((.....)))))..)))..)))).))))).. ( -32.80)
>consensus
CAAGGACCGUUUCGAGGUCCGUUUUAAAGGGUGUUCUCGGCCCGUUUUGGCUUGCUCUU_UUUAUUUACGGGCCAGAUGCACAAUUUGUUGUAAUACAAUAUUUUGGCCAUUAGGAGCCA
...(((((.......)))))((((..((.(((.......((....(((((((((..............))))))))).)).(((..(((((.....)))))..)))))).))..)))).. (-31.04 = -31.04 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	17,134,091 – 17,134,208
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.79
Mean single sequence MFE	-36.89
Consensus MFE	-32.74
Energy contribution	-32.66
Covariance contribution	-0.08
Combinations/Pair	1.09
Mean z-score	-1.17
Structure conservation index	0.89
SVM decision value	0.09
SVM RNA-class probability	0.578647
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17134091 117 - 22407834
GCCCCUUAGAUUUUUUGAUAAAUUUUCCAUAUCGUUAGCAGCAGC---AGCUGAUGAUGAGGAGCCAGAGGGGAGGACCACAAGGACCGUUUCGAGGUCCGUUUUAAAGGGUGUUUUCGG
.((((((((((((......))))))(((.((((((((((......---.)))))))))).)))....))))))((.(((....(((((.......))))).........))).))..... ( -37.22)
>DroSec_CAF1 102558 120 - 1
GCCCCUUAGAUUUUUUGAUAAAUUUUCCAUAUCGUUAGCAGCAGCGGCAGAUGAUGAUGAGGAGCCAGAGGGGAGGACCACAAGGACCGUUUCGAGGUCCGUUUUAAAGGGUGUUCUCGG
..(((((((((((......))))))(((.((((((((...((....))...)))))))).)))....)))))((((((.((..(((((.......)))))..........)))))))).. ( -35.50)
>DroSim_CAF1 114741 115 - 1
GCCCCUUAGAUUUUUUGAUAAAUUUUCCAUAUCGUUAGCAGCAGCGGCAGAUGAUGAUGAGGGGCCAGAGGGGAGGACCACAAGGACC-----GAGGUCCGUUUUAAAGGGUGUUCUCGG
(((((((((((((......))))).....(((((((.((.......)).))))))).)))))))).....(((((.(((....((((.-----...)))).........))).))))).. ( -37.32)
>DroEre_CAF1 100121 117 - 1
GCCCCUUAGAUUUUUUGAUAAAUUUUCCAUAUCGUUAGCAGCAGC---AGCUGAUGAUGAGGAGCCAGGGGGGAGGACCACAAGGACCGUUUCGAGGUCCGUUUUAAAGGGUGUUUUCUG
.(((((.((((((......))))))(((.((((((((((......---.)))))))))).)))...)))))(((((((.((..(((((.......)))))..........))))))))). ( -38.80)
>DroYak_CAF1 102464 115 - 1
GCCCCUUAGAUUUUUUGAUAAAUUUUCCAUAUCGUUAGCAGCAGC---AGCUGAUGAUGAGGAGCCAGAGGGGAGGACCACAAGGACCGUUUCGAGGUUCGUUUUAAAGGGUGU--UCUG
.((((((((((((......))))))(((.((((((((((......---.)))))))))).)))....)))))).(((.(((..(((((.......)))))..........))).--))). ( -35.60)
>consensus
GCCCCUUAGAUUUUUUGAUAAAUUUUCCAUAUCGUUAGCAGCAGC___AGCUGAUGAUGAGGAGCCAGAGGGGAGGACCACAAGGACCGUUUCGAGGUCCGUUUUAAAGGGUGUUCUCGG
.((((((((((((......))))))(((.((((((((((..........)))))))))).)))....))))))...(((....(((((.......))))).........)))........ (-32.74 = -32.66 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:14 2006