Locus 5069

Sequence ID	2R_DroMel_CAF1
Location	16,462,572 – 16,462,772
Length	200
Max. P	0.877404

overview

Window 3

Location	16,462,572 – 16,462,672
Length	100
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	69.54
Mean single sequence MFE	-42.48
Consensus MFE	-22.28
Energy contribution	-22.29
Covariance contribution	0.00
Combinations/Pair	1.25
Mean z-score	-1.71
Structure conservation index	0.52
SVM decision value	0.90
SVM RNA-class probability	0.877404
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16462572 100 - 20766785
AA---GCUAGUGCCUCAUCC---CACACCGCCGCAUGC---CACGCCCCCAGCGGGCGGCAACGGAGGCGGCGGACUGCUAACGGGCGGACUGAU------CUCGACGGCCGCCC
.(---((..(((........---))).(((((((...(---(..((((.....))))(....)))..)))))))...)))...((((((.(((..------.....))))))))) ( -47.20)
>DroPse_CAF1 171266 94 - 1
AAACCGCUCGUGCCUCAUCC------------CCACGC---CACGCCACCCUCGGGU------GGAGGCACCACCCUUAUCUCGGGUGGCCUGAUGCUCACUUCGACGGCAGCCC
...(((.(((.((.(((...------------....((---(...(((((....)))------)).))).((((((.......))))))..))).))......))))))...... ( -34.80)
>DroSec_CAF1 137899 100 - 1
AA---GCUAGUGCCUCAUCC---CACGCCGCCCCAUGC---CACGCCCCCAGAGGGCGGCAGCGGAGGCAGUGGACUGCUCACGGGCGGACUGAU------CUCGACGGCCGCCC
.(---((((.((((((....---...(((((((..((.---........))..)))))))....)))))).))).))......((((((.(((..------.....))))))))) ( -45.10)
>DroYak_CAF1 139618 100 - 1
AA---GCUAGUGCCUCAUCC---CACGCCGCCCCAUGC---CACGCCCCCAGCGGGCGGCAGCGGGGGCGACGGUCUGCUCACGGGCGGACUGAU------CUCGACGGCCGCCC
..---((..(((........---)))((((((((.(((---(..((((.....))))))))...)))))(((((((((((....))))))))).)------).....))).)).. ( -48.70)
>DroAna_CAF1 135122 106 - 1
AA---ACUGGUGGCCCAUCAGCAUCCCCCGCCACAUGCGGUCUCACCCUCCGGGGGC------GGUGCCACCACCCUGAUCUCGGGCGGCCUGAUGCUCACCUCUACGGCCGCCC
..---..(((((((((...........((((.....)))).....(((....)))..------)).)))))))..........((((((((.((........))...)))))))) ( -44.30)
>DroPer_CAF1 172201 94 - 1
AAACCGCUCGUGCCUCAUCC------------CCACGC---CACGCCACCCUCGGGU------GGAGGCACCACCCUUAUCUCGGGUGGCCUGAUGCUCACUUCGACGGCAGCCC
...(((.(((.((.(((...------------....((---(...(((((....)))------)).))).((((((.......))))))..))).))......))))))...... ( -34.80)
>consensus
AA___GCUAGUGCCUCAUCC___CAC_CCGCCCCAUGC___CACGCCCCCAGCGGGC______GGAGGCACCACCCUGAUCACGGGCGGACUGAU______CUCGACGGCCGCCC
..........((((((....................(......)((((.....)))).......)))))).............((((((.(((.............))))))))) (-22.28 = -22.29 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	16,462,672 – 16,462,772
Length	100
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	79.13
Mean single sequence MFE	-45.43
Consensus MFE	-29.98
Energy contribution	-30.87
Covariance contribution	0.89
Combinations/Pair	1.17
Mean z-score	-1.30
Structure conservation index	0.66
SVM decision value	0.10
SVM RNA-class probability	0.582294
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16462672 100 + 20766785
GGGACUCUCGCGCGGACUGCUGUUGCUGCACGGCGGGCUAACUUGGCUCAUCGCAGAGAGUCCUGCGUGCAGCGAUAGAUUCUGCGGAUAGCCGGCCGAU---
.((.((.((.((((((...(((((((((((((..(((((.....)))))..)((((......))))))))))))))))..)))))))).)))).......--- ( -48.90)
>DroGri_CAF1 163059 94 + 1
GGGACUUUCGCGAGGGCUGCUGUUGCUGCACGGCGGACUGACCUGCGCC---GACG------AUGGAUGCAGCGAGAGAUUCUGCGGGUAGCCGGCCGAGGCA
.((.(((((((.((((...((.(((((((((((((.(......).))))---).(.------...).)))))))).)).))))))))).)))).((....)). ( -35.00)
>DroSec_CAF1 137999 100 + 1
GGGACUCUCGCGCGGACUGCUGUUGCUGCACGGCGGGCUCACCUGGCUCAUUGCAGAGAGACCAGCGUGCAGCGAUAGAUUCUGCGGGUAGCCGGCCGAG---
.((.((..(.((((((...(((((((((((((.(.(((((..(((.(.....)))).))).)).))))))))))))))..)))))).).)))).......--- ( -45.60)
>DroEre_CAF1 139256 100 + 1
GGGACUCUCGCGCGGACUGCUGUUGCUGCAGGGCGGGCUCACCUGGCUCAUCGCGGAGAGUCCGGCGUGCAGCGAAAGGUUCUGCGGAUAGCCGGCGGAU---
.((.((.((.((((((((....((((((((.(.(((((((.((..((.....)))).))))))).).))))))))..)).)))))))).)))).......--- ( -49.30)
>DroYak_CAF1 139718 100 + 1
GGGACUCUCGCGCGGACUGCUGUUGCUGCAGGGCGGGCUCACCUGGCUCAUCGCCGAAAGAUUGGCGUGCAGCGACAGGUUCUGCGGAUAGCCGGCGGAA---
.((.((.((.((((((...((((((((((((((((((....))).))))..((((((....)))))))))))))))))..)))))))).)))).......--- ( -48.30)
>DroMoj_CAF1 226204 100 + 1
GGGGCUCUCCCGGGGACUGCUGUUGCUGCAGGGCGGGCUCACCUGCGCC---GACGACGACGACGAAUGCAGCGACAAGUUCUGCGGAUAGCCAACGGAGACA
..((((.(((..((((((..(((((((((((((((((....))))).))---..((....)).....))))))))))))))))..))).))))...(....). ( -45.50)
>consensus
GGGACUCUCGCGCGGACUGCUGUUGCUGCACGGCGGGCUCACCUGGCUCAUCGCCGAGAGACCGGCGUGCAGCGACAGAUUCUGCGGAUAGCCGGCCGAG___
.((.((.((.((((((...(((((((((((...((((....)))).(((......))).........)))))))))))..)))))))).)))).......... (-29.98 = -30.87 +   0.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:44 2006