Locus 114

Sequence ID	2L_DroMel_CAF1
Location	373,342 – 373,551
Length	209
Max. P	0.952983

overview

Window 9

Location	373,342 – 373,457
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.75
Mean single sequence MFE	-30.58
Consensus MFE	-27.46
Energy contribution	-27.46
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.66
Structure conservation index	0.90
SVM decision value	1.43
SVM RNA-class probability	0.952983
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 373342 115 - 22407834
UUUGCAGCAUUAAGAUGGGGUUC-----AAGCAUAAUUACUUUUUGUAAUUAGCUGCAGGUCCAAAGGGAGCCGAGCGAAAAGUUGGCAACGAGGGGCAUAAAGAUUGAUAACGAGCUAA
.(((((((.....((......))-----.....(((((((.....))))))))))))))((((...(...(((.(((.....))))))..)...))))...................... ( -28.90)
>DroSec_CAF1 41018 115 - 1
UUUGCAGCAUUAAAAUGGGGUUC-----AAGCAUAAUUACUUUUUGUAAUUAGCUGCAGGUCCAAAGGGAGCCGAGCGAAAAGUUGGCAACGAGGGGCAUAAAGAUUGAUAACGAGCUAA
.(((((((...........((..-----..)).(((((((.....))))))))))))))((((...(...(((.(((.....))))))..)...))))...................... ( -28.10)
>DroSim_CAF1 41678 115 - 1
UUUGCAGCAUUAAGAUGGGGUUC-----AAGCAUAAUUACUUUUUGUAAUUAGCUGCAGGUCCAAAGGGAGCCGAGCGAAAAGUUGGCAACGAGGGGCAUAAAGAUUGAUAACGAGCUAA
.(((((((.....((......))-----.....(((((((.....))))))))))))))((((...(...(((.(((.....))))))..)...))))...................... ( -28.90)
>DroEre_CAF1 47570 115 - 1
GUUGCAGCAUUAAGAUGGGGUUC-----AAGCAUAAUUACUUUUUGUAAUUAGCUGCAGGUCCAAAGGGAGCCGAGCGAAAAGUUGGCUACGAGGGGCAUAAAGAUUGAUAACGAGCUAA
.(((((((.....((......))-----.....(((((((.....))))))))))))))((((...(..((((.(((.....))))))).)...))))...................... ( -31.00)
>DroYak_CAF1 42183 120 - 1
GUUGCAGCAUUAAGAUGGGGUUCAACCCAAGCAUAAUUACUUUUUGUAAUUAGCUGCAGGUCCAAAAGGAGCCGAGCGAAAAGUUGGCAACGAGGGGCAUAAAGAUUGAUAACGAGCUAA
.(((((((.......((((......))))....(((((((.....))))))))))))))((((....(..(((.(((.....))))))..)...))))...................... ( -36.00)
>consensus
UUUGCAGCAUUAAGAUGGGGUUC_____AAGCAUAAUUACUUUUUGUAAUUAGCUGCAGGUCCAAAGGGAGCCGAGCGAAAAGUUGGCAACGAGGGGCAUAAAGAUUGAUAACGAGCUAA
.(((((((...........(((.......))).(((((((.....))))))))))))))((((....(..(((.(((.....))))))..)...))))...................... (-27.46 = -27.46 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	373,382 – 373,497
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.21
Mean single sequence MFE	-38.92
Consensus MFE	-36.16
Energy contribution	-36.40
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.14
Structure conservation index	0.93
SVM decision value	0.22
SVM RNA-class probability	0.639078
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 373382 115 - 22407834
GGCGAGUACCUCCUGCCCCUUGCGGUUCUUUGUGGCGCCGUUUGCAGCAUUAAGAUGGGGUUC-----AAGCAUAAUUACUUUUUGUAAUUAGCUGCAGGUCCAAAGGGAGCCGAGCGAA
((((.(.....).)))).....(((((((((.(((.(((...((((((.....((......))-----.....(((((((.....))))))))))))))))))).)))))))))...... ( -38.00)
>DroSec_CAF1 41058 115 - 1
GGCGAGUACCUCCUGCCCCUUGCGGUUCUUUGUGGCGCCGUUUGCAGCAUUAAAAUGGGGUUC-----AAGCAUAAUUACUUUUUGUAAUUAGCUGCAGGUCCAAAGGGAGCCGAGCGAA
((((.(.....).)))).....(((((((((.(((.(((...((((((...........((..-----..)).(((((((.....))))))))))))))))))).)))))))))...... ( -37.20)
>DroSim_CAF1 41718 115 - 1
GGCGAGUACCUCCUGCCCCUUGCGGUUCUUUGUGGCGCCGUUUGCAGCAUUAAGAUGGGGUUC-----AAGCAUAAUUACUUUUUGUAAUUAGCUGCAGGUCCAAAGGGAGCCGAGCGAA
((((.(.....).)))).....(((((((((.(((.(((...((((((.....((......))-----.....(((((((.....))))))))))))))))))).)))))))))...... ( -38.00)
>DroEre_CAF1 47610 115 - 1
GGCGAGUACCGCGUGCCCCUUGCGGUUCUUUGUGGCGCCGGUUGCAGCAUUAAGAUGGGGUUC-----AAGCAUAAUUACUUUUUGUAAUUAGCUGCAGGUCCAAAGGGAGCCGAGCGAA
.(((((.((((((.......))))))..)))))..(((((((((((((.....((......))-----.....(((((((.....)))))))))))))..(((....))))))).))).. ( -38.80)
>DroYak_CAF1 42223 120 - 1
GGCAAGUACCUCGUGCCCCUUGCAGUUCUCUGUGGCGCCGGUUGCAGCAUUAAGAUGGGGUUCAACCCAAGCAUAAUUACUUUUUGUAAUUAGCUGCAGGUCCAAAAGGAGCCGAGCGAA
((((.(.....).))))..(..(((....)))..)(((((((((((((.......((((......))))....(((((((.....)))))))))))))..(((....))))))).))).. ( -42.60)
>consensus
GGCGAGUACCUCCUGCCCCUUGCGGUUCUUUGUGGCGCCGUUUGCAGCAUUAAGAUGGGGUUC_____AAGCAUAAUUACUUUUUGUAAUUAGCUGCAGGUCCAAAGGGAGCCGAGCGAA
((((.(.....).))))..((((((((((((.(((.(((...((((((...........(((.......))).(((((((.....))))))))))))))))))).))))))))..)))). (-36.16 = -36.40 +   0.24)

alignment

secondary structure

dotplot

Window 1

Location	373,457 – 373,551
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	95.96
Mean single sequence MFE	-28.45
Consensus MFE	-22.01
Energy contribution	-22.89
Covariance contribution	0.88
Combinations/Pair	1.08
Mean z-score	-2.27
Structure conservation index	0.77
SVM decision value	0.59
SVM RNA-class probability	0.793203
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 373457 94 + 22407834
CGGCGCCACAAAGAACCGCAAGGGGCAGGAGGUACUCGCCCAGAGACCGCGUGAAAUCAAUAAAUUAAAUAUGCAAACUGCCCAUCGAUUGGCA
....((((....((..(....)((((((..(((.(((.....))))))(((((................)))))...)))))).))...)))). ( -30.29)
>DroSec_CAF1 41133 94 + 1
CGGCGCCACAAAGAACCGCAAGGGGCAGGAGGUACUCGCCGAGAGACCGCGUGAAAUCAAUAAAUUAAAUAUGCAAACUGCCCAUCGAUUGGCA
....((((....((..(....)((((((..(((.(((.....))))))(((((................)))))...)))))).))...)))). ( -30.29)
>DroSim_CAF1 41793 94 + 1
CGGCGCCACAAAGAACCGCAAGGGGCAGGAGGUACUCGCCCAGAGACCGCGUGAAAUCAAUAAAUUAAAUAUGCAAACUGCCCAUCGAUUGGCA
....((((....((..(....)((((((..(((.(((.....))))))(((((................)))))...)))))).))...)))). ( -30.29)
>DroEre_CAF1 47685 94 + 1
CGGCGCCACAAAGAACCGCAAGGGGCACGCGGUACUCGCCCAGAGUCCGCGUGAAAUCAAUAAAUUAAAUAUGCAAACUACCCAUCGAUUGGCA
....((((....((.((....))..(((((((.((((.....)))))))))))...............................))...)))). ( -30.60)
>DroYak_CAF1 42303 94 + 1
CGGCGCCACAGAGAACUGCAAGGGGCACGAGGUACUUGCCCAGAGUCCGCGUGAAAUCAAUAAAUUAAAUAUGCAAACUACCCAUCGAUUGGCA
....(((((((....)))...(((.((((.((.((((.....)))))).)))).(((......)))..............)))......)))). ( -20.80)
>consensus
CGGCGCCACAAAGAACCGCAAGGGGCAGGAGGUACUCGCCCAGAGACCGCGUGAAAUCAAUAAAUUAAAUAUGCAAACUGCCCAUCGAUUGGCA
....((((....((..(....)((((((..(((.(((.....))))))(((((................)))))...)))))).))...)))). (-22.01 = -22.89 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:26:14 2006