Locus 3198

Sequence ID	2R_DroMel_CAF1
Location	10,940,934 – 10,941,099
Length	165
Max. P	0.998532

overview

Window 7

Location	10,940,934 – 10,941,038
Length	104
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	99.23
Mean single sequence MFE	-32.40
Consensus MFE	-32.40
Energy contribution	-32.40
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.63
Structure conservation index	1.00
SVM decision value	1.55
SVM RNA-class probability	0.963571
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10940934 104 + 20766785
AUGUAAAAAUCUAUCUAGAGCUAGAGGCUCGGCUCGCUUUGCAUUUUGUAAUUUCGUGACCUUUGUGCCUGCACCGCACCACCCGAAUGUGGGUGCAGUCGCAA
.................((((.....))))((.((((.((((.....))))....)))))).(((((.(((((((.(((.........)))))))))).))))) ( -32.40)
>DroSec_CAF1 53649 104 + 1
AUGUAAAAAUCUAUCUAGAGCUAGAGGCUCGGCUCGCUUUGCAUUUUGUAAUUUCGUGACCUUUGUGCCUGCACCGCACCACCUGAAUGUGGGUGCAGUCGCAA
.................((((.....))))((.((((.((((.....))))....)))))).(((((.(((((((.(((.........)))))))))).))))) ( -32.40)
>DroSim_CAF1 55663 104 + 1
AUGUAAAAAUCUAUCUAGAGCUAGAGGCUCGGCUCGCUUUGCAUUUUGUAAUUUCGUGACCUUUGUGCCUGCACCGCACCACCCGAAUGUGGGUGCAGUCGCAA
.................((((.....))))((.((((.((((.....))))....)))))).(((((.(((((((.(((.........)))))))))).))))) ( -32.40)
>DroEre_CAF1 55206 104 + 1
AUGUAAAAAUCUAUCUAGAGCUAGAGGCUCGGCUCGCUUUGCAUUUUGUAAUUUCGUGACCUUUGUGCCUGCACCGCACCACCCGACUGUGGGUGCAGUCGCAA
.................((((.....))))((.((((.((((.....))))....)))))).(((((.(((((((.(((.........)))))))))).))))) ( -32.40)
>DroYak_CAF1 55803 104 + 1
AUGUAAAAAUCUAUCUAGAGCUAGAGGCUCGGCUCGCUUUGCAUUUUGUAAUUUCGUGACCUUUGUGCCUGCACCGCACCACCCGAAUGUGGGUGCAGUCGCAA
.................((((.....))))((.((((.((((.....))))....)))))).(((((.(((((((.(((.........)))))))))).))))) ( -32.40)
>consensus
AUGUAAAAAUCUAUCUAGAGCUAGAGGCUCGGCUCGCUUUGCAUUUUGUAAUUUCGUGACCUUUGUGCCUGCACCGCACCACCCGAAUGUGGGUGCAGUCGCAA
.................((((.....))))((.((((.((((.....))))....)))))).(((((.(((((((.(((.........)))))))))).))))) (-32.40 = -32.40 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	10,940,966 – 10,941,068
Length	102
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	98.82
Mean single sequence MFE	-27.80
Consensus MFE	-27.80
Energy contribution	-27.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.58
Structure conservation index	1.00
SVM decision value	1.53
SVM RNA-class probability	0.961509
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10940966 102 + 20766785
CUCGCUUUGCAUUUUGUAAUUUCGUGACCUUUGUGCCUGCACCGCACCACCCGAAUGUGGGUGCAGUCGCAAUAGCACCCGUACACGUACUUGUAACCACAA
......(((((...((((.....(((.(..(((((.(((((((.(((.........)))))))))).)))))..))))...))))......)))))...... ( -27.80)
>DroSec_CAF1 53681 102 + 1
CUCGCUUUGCAUUUUGUAAUUUCGUGACCUUUGUGCCUGCACCGCACCACCUGAAUGUGGGUGCAGUCGCAAUAGCACCCGUACACGUACUUGUAACCACCA
......(((((...((((.....(((.(..(((((.(((((((.(((.........)))))))))).)))))..))))...))))......)))))...... ( -27.80)
>DroSim_CAF1 55695 102 + 1
CUCGCUUUGCAUUUUGUAAUUUCGUGACCUUUGUGCCUGCACCGCACCACCCGAAUGUGGGUGCAGUCGCAAUAGCACCCGUACACGUACUUGUAACCACCA
......(((((...((((.....(((.(..(((((.(((((((.(((.........)))))))))).)))))..))))...))))......)))))...... ( -27.80)
>DroEre_CAF1 55238 102 + 1
CUCGCUUUGCAUUUUGUAAUUUCGUGACCUUUGUGCCUGCACCGCACCACCCGACUGUGGGUGCAGUCGCAAUAGCACCCGUACACGUACUUGUAACCACCA
......(((((...((((.....(((.(..(((((.(((((((.(((.........)))))))))).)))))..))))...))))......)))))...... ( -27.80)
>DroYak_CAF1 55835 102 + 1
CUCGCUUUGCAUUUUGUAAUUUCGUGACCUUUGUGCCUGCACCGCACCACCCGAAUGUGGGUGCAGUCGCAAUAGCACCCGUACACGUACUUGUAACCACCA
......(((((...((((.....(((.(..(((((.(((((((.(((.........)))))))))).)))))..))))...))))......)))))...... ( -27.80)
>consensus
CUCGCUUUGCAUUUUGUAAUUUCGUGACCUUUGUGCCUGCACCGCACCACCCGAAUGUGGGUGCAGUCGCAAUAGCACCCGUACACGUACUUGUAACCACCA
......(((((...((((.....(((.(..(((((.(((((((.(((.........)))))))))).)))))..))))...))))......)))))...... (-27.80 = -27.80 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	10,940,966 – 10,941,068
Length	102
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	98.82
Mean single sequence MFE	-31.96
Consensus MFE	-31.70
Energy contribution	-31.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.17
Structure conservation index	0.99
SVM decision value	0.08
SVM RNA-class probability	0.573341
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10940966 102 - 20766785
UUGUGGUUACAAGUACGUGUACGGGUGCUAUUGCGACUGCACCCACAUUCGGGUGGUGCGGUGCAGGCACAAAGGUCACGAAAUUACAAAAUGCAAAGCGAG
((((.((.....(((((((..(..(((((..(((.((((((((.((......))))))))))))))))))...)..))))....))).....))...)))). ( -33.00)
>DroSec_CAF1 53681 102 - 1
UGGUGGUUACAAGUACGUGUACGGGUGCUAUUGCGACUGCACCCACAUUCAGGUGGUGCGGUGCAGGCACAAAGGUCACGAAAUUACAAAAUGCAAAGCGAG
..((.((.....(((((((..(..(((((..(((.((((((((.((......))))))))))))))))))...)..))))....))).....))...))... ( -31.70)
>DroSim_CAF1 55695 102 - 1
UGGUGGUUACAAGUACGUGUACGGGUGCUAUUGCGACUGCACCCACAUUCGGGUGGUGCGGUGCAGGCACAAAGGUCACGAAAUUACAAAAUGCAAAGCGAG
..((.((.....(((((((..(..(((((..(((.((((((((.((......))))))))))))))))))...)..))))....))).....))...))... ( -31.70)
>DroEre_CAF1 55238 102 - 1
UGGUGGUUACAAGUACGUGUACGGGUGCUAUUGCGACUGCACCCACAGUCGGGUGGUGCGGUGCAGGCACAAAGGUCACGAAAUUACAAAAUGCAAAGCGAG
..((.((.....(((((((..(..(((((..(((.((((((((.((......))))))))))))))))))...)..))))....))).....))...))... ( -31.70)
>DroYak_CAF1 55835 102 - 1
UGGUGGUUACAAGUACGUGUACGGGUGCUAUUGCGACUGCACCCACAUUCGGGUGGUGCGGUGCAGGCACAAAGGUCACGAAAUUACAAAAUGCAAAGCGAG
..((.((.....(((((((..(..(((((..(((.((((((((.((......))))))))))))))))))...)..))))....))).....))...))... ( -31.70)
>consensus
UGGUGGUUACAAGUACGUGUACGGGUGCUAUUGCGACUGCACCCACAUUCGGGUGGUGCGGUGCAGGCACAAAGGUCACGAAAUUACAAAAUGCAAAGCGAG
..((.((.....(((((((..(..(((((..(((.((((((((.((......))))))))))))))))))...)..))))....))).....))...))... (-31.70 = -31.70 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	10,940,999 – 10,941,099
Length	100
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	92.73
Mean single sequence MFE	-17.92
Consensus MFE	-17.50
Energy contribution	-17.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.84
Structure conservation index	0.98
SVM decision value	3.13
SVM RNA-class probability	0.998532
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10940999 100 + 20766785
UGCCUGCACCGCACCACCCGAAUGUGGGUGCAGUCGCAAUAGCACCCGUACACGUACUUGUAACCACAAAAUAC------UACCAACUACCAACCACCCACA--ACAC
((((((((((.(((.........))))))))))..))).........(((....)))((((....)))).....------......................--.... ( -17.60)
>DroSec_CAF1 53714 93 + 1
UGCCUGCACCGCACCACCUGAAUGUGGGUGCAGUCGCAAUAGCACCCGUACACGUACUUGUAACCACCAAAUAC------UAC-------CAACCACCCACA--ACAC
((((((((((.(((.........))))))))))..)))...............(((.(((.......))).)))------...-------............--.... ( -17.80)
>DroSim_CAF1 55728 93 + 1
UGCCUGCACCGCACCACCCGAAUGUGGGUGCAGUCGCAAUAGCACCCGUACACGUACUUGUAACCACCAAAUAC------UAC-------CAACCACCCACA--ACAC
((((((((((.(((.........))))))))))..)))...............(((.(((.......))).)))------...-------............--.... ( -17.80)
>DroEre_CAF1 55271 93 + 1
UGCCUGCACCGCACCACCCGACUGUGGGUGCAGUCGCAAUAGCACCCGUACACGUACUUGUAACCACCAAAUAC------UAC-------CAACCACCCACA--ACAC
((((((((((.(((.........))))))))))..)))...............(((.(((.......))).)))------...-------............--.... ( -17.80)
>DroYak_CAF1 55868 101 + 1
UGCCUGCACCGCACCACCCGAAUGUGGGUGCAGUCGCAAUAGCACCCGUACACGUACUUGUAACCACCAAAUACUACUACUAC-------CAACCACCCACAAAACAC
((((((((((.(((.........))))))))))..))).........(((...(((.(((.......))).)))...)))...-------.................. ( -18.60)
>consensus
UGCCUGCACCGCACCACCCGAAUGUGGGUGCAGUCGCAAUAGCACCCGUACACGUACUUGUAACCACCAAAUAC______UAC_______CAACCACCCACA__ACAC
((((((((((.(((.........))))))))))..)))...(((...(((....))).)))............................................... (-17.50 = -17.50 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:49 2006