Locus 5177

Sequence ID	3L_DroMel_CAF1
Location	14,256,837 – 14,256,929
Length	92
Max. P	0.700588

overview

Window 7

Location	14,256,837 – 14,256,929
Length	92
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	80.41
Mean single sequence MFE	-21.42
Consensus MFE	-14.87
Energy contribution	-15.07
Covariance contribution	0.19
Combinations/Pair	1.13
Mean z-score	-1.49
Structure conservation index	0.69
SVM decision value	0.35
SVM RNA-class probability	0.700588
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14256837 92 + 23771897
GCUUUCUCAGUUCACUC-UU---------UCAUGUAUAGGUGCGUUGGGCAACGCAUUUUUGCAUGCUCCAUCCGCCACGCCCCAAAAACACCUACCACGCC----
.................-..---------....((.((((((..((((((...(((....)))..((.......))...).)))))...))))))..))...---- ( -19.10)
>DroSec_CAF1 87369 92 + 1
GUUUUCUCAGUUCACUC-UU---------UCGUGUAUAGGUGCGUUGGGCAACGCAUUUUUGCAUGCUCCAUCCGCCACGCCCCAAAAACACCUACCACGCC----
.................-..---------..((((.((((((..((((((...(((....)))..((.......))...).)))))...))))))..)))).---- ( -22.40)
>DroSim_CAF1 87492 92 + 1
GUUUUCUCAGUUCACUC-UU---------UCGUGUAUAGGUGCGUUGGGCAACGCAUUUUUGCAUGCUCCAUCCGCCACGCCCCAAAAACACCUACCACGCC----
.................-..---------..((((.((((((..((((((...(((....)))..((.......))...).)))))...))))))..)))).---- ( -22.40)
>DroEre_CAF1 86671 93 + 1
GCCUUCUCCGUUCACUCCGU---------UCCUGUAUAGGUGCGUUGGCCAACGCAUUUUUGCAUGCUCCAUCCGCCACGCCCCAAGAACACCUACCACGCC----
.........((((((.....---------....))...((.((((.(((....((((......)))).......))))))).))..))))............---- ( -18.00)
>DroYak_CAF1 90239 92 + 1
GCUUUCUCCGUUCACUC-UU---------UCAUGCAGAGGUGCGUUGGGCAACGCAUUUUUGCAUGCUCCAUCCGCCACGCCCCAAAAACACCUACCACGCC----
.................-..---------.((((((((((((((((....))))))))))))))))....................................---- ( -22.30)
>DroAna_CAF1 83516 92 + 1
---UCCCCCCAACACUC-UGUGGGAUUUCGCAUUUAUAGGUGCGAUGGGUAACGCAUUUCUGCAUGCUCUGUACACCAC----------CACCGCCCACGAUAUCC
---..............-((((((...(((((((....)))))))((((((..((((......))))....))).))).----------.....))))))...... ( -24.30)
>consensus
GCUUUCUCAGUUCACUC_UU_________UCAUGUAUAGGUGCGUUGGGCAACGCAUUUUUGCAUGCUCCAUCCGCCACGCCCCAAAAACACCUACCACGCC____
..............................((((((.(((((((((....))))))))).))))))........................................ (-14.87 = -15.07 +   0.19)

alignment

secondary structure

dotplot

Window 8

Location	14,256,837 – 14,256,929
Length	92
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	80.41
Mean single sequence MFE	-28.52
Consensus MFE	-20.20
Energy contribution	-21.73
Covariance contribution	1.53
Combinations/Pair	1.08
Mean z-score	-1.29
Structure conservation index	0.71
SVM decision value	0.16
SVM RNA-class probability	0.610337
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14256837 92 - 23771897
----GGCGUGGUAGGUGUUUUUGGGGCGUGGCGGAUGGAGCAUGCAAAAAUGCGUUGCCCAACGCACCUAUACAUGA---------AA-GAGUGAACUGAGAAAGC
----..((((((((((((.....(((((..((.......))(((((....))))))))))...)))))))).)))).---------..-.((....))........ ( -27.80)
>DroSec_CAF1 87369 92 - 1
----GGCGUGGUAGGUGUUUUUGGGGCGUGGCGGAUGGAGCAUGCAAAAAUGCGUUGCCCAACGCACCUAUACACGA---------AA-GAGUGAACUGAGAAAAC
----..((((((((((((.....(((((..((.......))(((((....))))))))))...)))))))).)))).---------..-.((....))........ ( -29.60)
>DroSim_CAF1 87492 92 - 1
----GGCGUGGUAGGUGUUUUUGGGGCGUGGCGGAUGGAGCAUGCAAAAAUGCGUUGCCCAACGCACCUAUACACGA---------AA-GAGUGAACUGAGAAAAC
----..((((((((((((.....(((((..((.......))(((((....))))))))))...)))))))).)))).---------..-.((....))........ ( -29.60)
>DroEre_CAF1 86671 93 - 1
----GGCGUGGUAGGUGUUCUUGGGGCGUGGCGGAUGGAGCAUGCAAAAAUGCGUUGGCCAACGCACCUAUACAGGA---------ACGGAGUGAACGGAGAAGGC
----..(((......(((((((((((((((((.(((...((((......))))))).))).)))).))....)))))---------)))......)))........ ( -29.60)
>DroYak_CAF1 90239 92 - 1
----GGCGUGGUAGGUGUUUUUGGGGCGUGGCGGAUGGAGCAUGCAAAAAUGCGUUGCCCAACGCACCUCUGCAUGA---------AA-GAGUGAACGGAGAAAGC
----.(((..(.((((((.....(((((..((.......))(((((....))))))))))...)))))))..)....---------..-..(....).......)) ( -26.10)
>DroAna_CAF1 83516 92 - 1
GGAUAUCGUGGGCGGUG----------GUGGUGUACAGAGCAUGCAGAAAUGCGUUACCCAUCGCACCUAUAAAUGCGAAAUCCCACA-GAGUGUUGGGGGGA---
.....((((((((((((----------(.(((((.....))))(((....)))....)))))))).)).......))))..((((.((-(....)))..))))--- ( -28.41)
>consensus
____GGCGUGGUAGGUGUUUUUGGGGCGUGGCGGAUGGAGCAUGCAAAAAUGCGUUGCCCAACGCACCUAUACAUGA_________AA_GAGUGAACGGAGAAAGC
......((((((((((((.....(((((..((.......))(((((....))))))))))...)))))))).)))).............................. (-20.20 = -21.73 +   1.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:51 2006