Locus 5371

Sequence ID	3L_DroMel_CAF1
Location	14,781,392 – 14,781,578
Length	186
Max. P	0.975315

overview

Window 2

Location	14,781,392 – 14,781,508
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	94.26
Mean single sequence MFE	-36.65
Consensus MFE	-32.18
Energy contribution	-32.73
Covariance contribution	0.56
Combinations/Pair	1.06
Mean z-score	-1.47
Structure conservation index	0.88
SVM decision value	0.45
SVM RNA-class probability	0.742318
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14781392 116 + 23771897
UUGACGCCCCCACACAG----CAGCUGGCCAAAAACUCGUUGGCAAGCUUAUUGUCAACUAUUUAAAUGCUGCAAUUUCGGUCUUUUGUGCAGCUGGAAUGUGUGAGGCCCGAGCAGCCA
.....(((..((((((.----((((((..(((((....((((((((.....)))))))).........((((......)))).)))))..))))))...)))))).)))........... ( -36.50)
>DroSec_CAF1 24332 120 + 1
UUGACGCCCCCACACAGCAAGCAGCUGGCCAAAAACUCGUUGGCAAGCUUAUUGUCAACUAUUUAAAUGCUGCAAUUUCGGUCUUUUGUUCAGCUGGAAUGUGUGAGGCCCGAGCAGCCA
.....(((..((((((.....((((((..(((((....((((((((.....)))))))).........((((......)))).)))))..))))))...)))))).)))........... ( -37.90)
>DroSim_CAF1 16505 120 + 1
UUGACGCCCCCACACAGCAAGCAGCUGGCCAAAAACUCGUUGGCAAGCUUAUUGUCAACUAUUUAAAUGCUGCAAUUUCGGUCUUUUGUGCAGCUGGAAUGUGUGAGGCCCGAGCAGCCA
.....(((..((((((.....((((((..(((((....((((((((.....)))))))).........((((......)))).)))))..))))))...)))))).)))........... ( -35.90)
>DroEre_CAF1 23618 114 + 1
UUGACGCC--CACACAG----CAGCUGGCCAAAAACUCGUUGGCAAGCUUAUUGUCAACUAUUUAAAUGCUGCAAUUUCGGUCUUUUGUGCAGCUGGAAUGUGUGAGGCCCGAGCAGCCA
.....(((--((((((.----((((((..(((((....((((((((.....)))))))).........((((......)))).)))))..))))))...)))))).)))........... ( -37.70)
>DroYak_CAF1 24554 116 + 1
UUGACGCCCCCACACAG----CAGCUGGCCAAAAACUCGUUGGCAAGCUUAUUGUCAACUAUUUAAAUGCUGCAAUUUCGGCCUUUUGUGCAGCUGGAAUGUGUGAGGCCCGAGCAGCCA
.....(((..((((((.----((((((..(((((....((((((((.....)))))))).........((((......)))).)))))..))))))...)))))).)))........... ( -38.40)
>DroAna_CAF1 24036 113 + 1
UCACCACCCCCG--CAG----CAGCUGGCCAA-AACUCGUUGGCAAGCUUAUUGUCAACUAUUUAAAUGCUGCAAUUUCGGUCUUUUGUGCAGGCGGAAUGUGUGAGGCCCGAGCAGCCA
((((((...(((--(.(----(((..((((..-.....((((((((.....)))))))).....((((......)))).))))..))))....))))..)).))))(((.......))). ( -33.50)
>consensus
UUGACGCCCCCACACAG____CAGCUGGCCAAAAACUCGUUGGCAAGCUUAUUGUCAACUAUUUAAAUGCUGCAAUUUCGGUCUUUUGUGCAGCUGGAAUGUGUGAGGCCCGAGCAGCCA
..........((((((.....((((((..(((((....((((((((.....)))))))).........((((......)))).)))))..))))))...)))))).(((.......))). (-32.18 = -32.73 +   0.56)

alignment

secondary structure

dotplot

Window 3

Location	14,781,428 – 14,781,548
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	98.89
Mean single sequence MFE	-32.64
Consensus MFE	-30.96
Energy contribution	-31.29
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.25
Structure conservation index	0.95
SVM decision value	1.23
SVM RNA-class probability	0.933131
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14781428 120 + 23771897
UGGCAAGCUUAUUGUCAACUAUUUAAAUGCUGCAAUUUCGGUCUUUUGUGCAGCUGGAAUGUGUGAGGCCCGAGCAGCCAUUACACUUGUGGCCAUUGUUUGCCUUUAUAGCCUUUUGUU
.(((((((......(((..(((((....((((((..............))))))..)))))..)))((((((((...........)))).))))...)))))))................ ( -33.04)
>DroSec_CAF1 24372 120 + 1
UGGCAAGCUUAUUGUCAACUAUUUAAAUGCUGCAAUUUCGGUCUUUUGUUCAGCUGGAAUGUGUGAGGCCCGAGCAGCCAUUACACUUGUGGCCAUUGUUUGCCUUUAUAGCCUUUUGUU
.(((((((..((.((((...........(((((....((((((((.(((((.....)))))...)))).)))))))))...........)))).)).)))))))................ ( -31.25)
>DroSim_CAF1 16545 120 + 1
UGGCAAGCUUAUUGUCAACUAUUUAAAUGCUGCAAUUUCGGUCUUUUGUGCAGCUGGAAUGUGUGAGGCCCGAGCAGCCAUUACACUUGUGGCCAUUGUUUGCCUUUAUAGCCUUUUGUU
.(((((((......(((..(((((....((((((..............))))))..)))))..)))((((((((...........)))).))))...)))))))................ ( -33.04)
>DroEre_CAF1 23652 120 + 1
UGGCAAGCUUAUUGUCAACUAUUUAAAUGCUGCAAUUUCGGUCUUUUGUGCAGCUGGAAUGUGUGAGGCCCGAGCAGCCAUUACACUUGUGGCCAUUGUUUGCCUUUAUAGCCUUUUGUU
.(((((((......(((..(((((....((((((..............))))))..)))))..)))((((((((...........)))).))))...)))))))................ ( -33.04)
>DroYak_CAF1 24590 120 + 1
UGGCAAGCUUAUUGUCAACUAUUUAAAUGCUGCAAUUUCGGCCUUUUGUGCAGCUGGAAUGUGUGAGGCCCGAGCAGCCAUUACACUUGUGGCCAUUGUUUGCCUUUAUAGCCUUUUGUU
.(((((((..((.((((...........(((((....((((((((..(..((.......))..))))).)))))))))...........)))).)).)))))))................ ( -33.45)
>DroAna_CAF1 24069 120 + 1
UGGCAAGCUUAUUGUCAACUAUUUAAAUGCUGCAAUUUCGGUCUUUUGUGCAGGCGGAAUGUGUGAGGCCCGAGCAGCCAUUACACUUGUGGCCAUUGUUUGCCUUUAUAGCCUUUUGUU
.(((((((...................(((.((((..........)))))))(((.(...(((((((((.......))).))))))...).)))...)))))))................ ( -32.00)
>consensus
UGGCAAGCUUAUUGUCAACUAUUUAAAUGCUGCAAUUUCGGUCUUUUGUGCAGCUGGAAUGUGUGAGGCCCGAGCAGCCAUUACACUUGUGGCCAUUGUUUGCCUUUAUAGCCUUUUGUU
.(((((((......(((..(((((....((((((..............))))))..)))))..)))((((((((...........)))).))))...)))))))................ (-30.96 = -31.29 +   0.33)

alignment

secondary structure

dotplot

Window 4

Location	14,781,428 – 14,781,548
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	98.89
Mean single sequence MFE	-27.29
Consensus MFE	-25.82
Energy contribution	-26.16
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.47
Structure conservation index	0.95
SVM decision value	1.75
SVM RNA-class probability	0.975315
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14781428 120 - 23771897
AACAAAAGGCUAUAAAGGCAAACAAUGGCCACAAGUGUAAUGGCUGCUCGGGCCUCACACAUUCCAGCUGCACAAAAGACCGAAAUUGCAGCAUUUAAAUAGUUGACAAUAAGCUUGCCA
.......(((......(((........))).(((((((...((((.....))))..))))......((((((..............))))))..........)))...........))). ( -28.04)
>DroSec_CAF1 24372 120 - 1
AACAAAAGGCUAUAAAGGCAAACAAUGGCCACAAGUGUAAUGGCUGCUCGGGCCUCACACAUUCCAGCUGAACAAAAGACCGAAAUUGCAGCAUUUAAAUAGUUGACAAUAAGCUUGCCA
.......(((......(((........)))....((((...((((.....))))..)))).....((((...(....)......((((((((.........)))).)))).)))).))). ( -24.20)
>DroSim_CAF1 16545 120 - 1
AACAAAAGGCUAUAAAGGCAAACAAUGGCCACAAGUGUAAUGGCUGCUCGGGCCUCACACAUUCCAGCUGCACAAAAGACCGAAAUUGCAGCAUUUAAAUAGUUGACAAUAAGCUUGCCA
.......(((......(((........))).(((((((...((((.....))))..))))......((((((..............))))))..........)))...........))). ( -28.04)
>DroEre_CAF1 23652 120 - 1
AACAAAAGGCUAUAAAGGCAAACAAUGGCCACAAGUGUAAUGGCUGCUCGGGCCUCACACAUUCCAGCUGCACAAAAGACCGAAAUUGCAGCAUUUAAAUAGUUGACAAUAAGCUUGCCA
.......(((......(((........))).(((((((...((((.....))))..))))......((((((..............))))))..........)))...........))). ( -28.04)
>DroYak_CAF1 24590 120 - 1
AACAAAAGGCUAUAAAGGCAAACAAUGGCCACAAGUGUAAUGGCUGCUCGGGCCUCACACAUUCCAGCUGCACAAAAGGCCGAAAUUGCAGCAUUUAAAUAGUUGACAAUAAGCUUGCCA
................(((((.(..(((((....((((...(((((....(........)....)))))))))....)))))..((((((((.........)))).))))..).))))). ( -29.90)
>DroAna_CAF1 24069 120 - 1
AACAAAAGGCUAUAAAGGCAAACAAUGGCCACAAGUGUAAUGGCUGCUCGGGCCUCACACAUUCCGCCUGCACAAAAGACCGAAAUUGCAGCAUUUAAAUAGUUGACAAUAAGCUUGCCA
.......(((.....((((......((....)).((((...((((.....))))..)))).....))))...............((((((((.........)))).))))......))). ( -25.50)
>consensus
AACAAAAGGCUAUAAAGGCAAACAAUGGCCACAAGUGUAAUGGCUGCUCGGGCCUCACACAUUCCAGCUGCACAAAAGACCGAAAUUGCAGCAUUUAAAUAGUUGACAAUAAGCUUGCCA
.......(((......(((........))).(((((((...((((.....))))..))))......((((((..............))))))..........)))...........))). (-25.82 = -26.16 +   0.33)

alignment

secondary structure

dotplot

Window 5

Location	14,781,468 – 14,781,578
Length	110
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	91.87
Mean single sequence MFE	-28.50
Consensus MFE	-27.45
Energy contribution	-27.78
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.40
Structure conservation index	0.96
SVM decision value	1.67
SVM RNA-class probability	0.970853
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14781468 110 + 23771897
GUCUUUUGUGCAGCUGGAAUGUGUGAGGCCCGAGCAGCCAUUACACUUGUGGCCAUUGUUUGCCUUUAUAGCCUUUUGUUGCAUAAAUCGUUUACUACAAUAAAA----AAAAA------
....((((((((((.((..((((.(((((..((((((((((.......)))))...))))))))))))))..))...))))))))))..................----.....------ ( -29.50)
>DroSec_CAF1 24412 104 + 1
GUCUUUUGUUCAGCUGGAAUGUGUGAGGCCCGAGCAGCCAUUACACUUGUGGCCAUUGUUUGCCUUUAUAGCCUUUUGUUGCAUAAAUCGUUUACUACAAUAAA----------------
....(((((.((((.((..((((.(((((..((((((((((.......)))))...))))))))))))))..))...)))).))))).................---------------- ( -22.90)
>DroSim_CAF1 16585 104 + 1
GUCUUUUGUGCAGCUGGAAUGUGUGAGGCCCGAGCAGCCAUUACACUUGUGGCCAUUGUUUGCCUUUAUAGCCUUUUGUUGCAUAAAUCGUUUACUACAAUAAA----------------
....((((((((((.((..((((.(((((..((((((((((.......)))))...))))))))))))))..))...)))))))))).................---------------- ( -29.50)
>DroEre_CAF1 23692 116 + 1
GUCUUUUGUGCAGCUGGAAUGUGUGAGGCCCGAGCAGCCAUUACACUUGUGGCCAUUGUUUGCCUUUAUAGCCUUUUGUUGCAUAAAUCGUUUACUACAAUAAAA----AAAAAAACAAA
....((((((((((.((..((((.(((((..((((((((((.......)))))...))))))))))))))..))...))))))))))..................----........... ( -29.50)
>DroYak_CAF1 24630 106 + 1
GCCUUUUGUGCAGCUGGAAUGUGUGAGGCCCGAGCAGCCAUUACACUUGUGGCCAUUGUUUGCCUUUAUAGCCUUUUGUUGCAUAAAUCGUUUACUACAAUAAAA----A----------
((..((((((((((.((..((((.(((((..((((((((((.......)))))...))))))))))))))..))...))))))))))..))..............----.---------- ( -30.20)
>DroAna_CAF1 24109 114 + 1
GUCUUUUGUGCAGGCGGAAUGUGUGAGGCCCGAGCAGCCAUUACACUUGUGGCCAUUGUUUGCCUUUAUAGCCUUUUGUUGCAUAAAUCGUUUACAACAAUACAGCAGCAGAAA------
...((((((((.(((.(...(((((((((.......))).))))))...).))).((((..((.(((((.((........)))))))..))..)))).......))).))))).------ ( -29.40)
>consensus
GUCUUUUGUGCAGCUGGAAUGUGUGAGGCCCGAGCAGCCAUUACACUUGUGGCCAUUGUUUGCCUUUAUAGCCUUUUGUUGCAUAAAUCGUUUACUACAAUAAAA____A__________
....((((((((((.((..((((.(((((..((((((((((.......)))))...))))))))))))))..))...))))))))))................................. (-27.45 = -27.78 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:35 2006