Locus 4609

Sequence ID	2L_DroMel_CAF1
Location	13,189,873 – 13,190,142
Length	269
Max. P	0.974130

overview

Window 2

Location	13,189,873 – 13,189,992
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.42
Mean single sequence MFE	-29.82
Consensus MFE	-24.70
Energy contribution	-24.57
Covariance contribution	-0.13
Combinations/Pair	1.08
Mean z-score	-2.08
Structure conservation index	0.83
SVM decision value	0.59
SVM RNA-class probability	0.790871
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13189873 119 + 22407834
GGCAACGGACAAAAUCAAUAAGUUAGGUAAAUAACAUAAAUAAAACGGUGGUCUAAAGGAGGCGGAGGACGCGACGUCCAGUUGCGCGUCCAAAUGGCGACGCACAGA-AAUGUUUGGAA
.(((((((((...........((((......))))..........................(((.....)))...)))).)))))(((((........)))))(((..-..)))...... ( -29.90)
>DroSec_CAF1 10268 119 + 1
GGCAAUGGACAAAAUCAAUAAGUUAGGUAAAUAAUAUAAAUAAAACGGUGGUCUAAAGGAGGCGGAGGACGCGCAGUCCAGUUGCGUGUCCAAAUGGCGACGCACAGA-AAUGUGUGGAA
.((..(((((...(((......(((.(((.....)))...)))...))).)))))...........((((((((((.....)))))))))).....))..((((((..-..))))))... ( -33.00)
>DroSim_CAF1 10249 119 + 1
GGCAAUGGACAAAAUCAAUAAGUUAGGUAAAUAAUAUAAAUAAAACGGUGGUCUAAAGGAGGCGGAGGACGCACAGUCCAGUUGCGUGUCCAAAUGGCGACGCACAGA-AAUGUGUGGAA
.((..((((((....((((...............................((((.....))))...((((.....)))).))))..))))))....))..((((((..-..))))))... ( -31.10)
>DroYak_CAF1 10383 120 + 1
UGGAAUGAACAAAAUCAAUAAGUUAGGUAAAUAAUAUAAAUAAAACAGUGGUCUAAAGGAGGCGGAGGACGCACAGUCCAGUUGCGUGUCCAAUUGGCGACGCACAGAAAAUGUGUGGAA
..............((...............................((.(((....(((.(((.(((((.....))))...).))).)))....))).))(((((.....))))).)). ( -25.30)
>consensus
GGCAAUGGACAAAAUCAAUAAGUUAGGUAAAUAAUAUAAAUAAAACGGUGGUCUAAAGGAGGCGGAGGACGCACAGUCCAGUUGCGUGUCCAAAUGGCGACGCACAGA_AAUGUGUGGAA
.....................((((......))))............((.(((....(((.(((.(((((.....))))...).))).)))....))).))(((((.....))))).... (-24.70 = -24.57 +  -0.13)

alignment

secondary structure

dotplot

Window 3

Location	13,189,913 – 13,190,032
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.74
Mean single sequence MFE	-35.95
Consensus MFE	-29.06
Energy contribution	-29.00
Covariance contribution	-0.06
Combinations/Pair	1.10
Mean z-score	-1.82
Structure conservation index	0.81
SVM decision value	0.49
SVM RNA-class probability	0.754914
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13189913 119 + 22407834
UAAAACGGUGGUCUAAAGGAGGCGGAGGACGCGACGUCCAGUUGCGCGUCCAAAUGGCGACGCACAGA-AAUGUUUGGAACCGUAAAGAGGUGGAACUUUUGUAGUAUUCUUCUUUUAAU
....(((((..(((((.....(((((.(.((((((.....))))))).)))....(....)))(((..-..)))))))))))))(((((((....(((.....)))...))))))).... ( -34.50)
>DroSec_CAF1 10308 116 + 1
UAAAACGGUGGUCUAAAGGAGGCGGAGGACGCGCAGUCCAGUUGCGUGUCCAAAUGGCGACGCACAGA-AAUGUGUGGAACCGUAAAGUGAGGGAACUUUUGUAGCAUUC---UUUUAAU
.............((((((((((...((((((((((.....))))))))))..((((...((((((..-..))))))...))))(((((......)))))....)).)))---))))).. ( -40.20)
>DroSim_CAF1 10289 116 + 1
UAAAACGGUGGUCUAAAGGAGGCGGAGGACGCACAGUCCAGUUGCGUGUCCAAAUGGCGACGCACAGA-AAUGUGUGGAACCGUAAAGUGAGGGAACUUUUGUAGCAUUC---UUUUAAU
....(((((.(((....(((.(((.(((((.....))))...).))).)))....)))..((((((..-..))))))..)))))....((((((((((.....))..)))---))))).. ( -36.30)
>DroYak_CAF1 10423 119 + 1
UAAAACAGUGGUCUAAAGGAGGCGGAGGACGCACAGUCCAGUUGCGUGUCCAAUUGGCGACGCACAGAAAAUGUGUGGAACCAUAAAGUGAGGGAACUUUUGUAGUAUUCUUC-UUAAAU
.......(((((.....(((.(((.(((((.....))))...).))).))).........((((((.....))))))..))))).....(((((((((.....))).))))))-...... ( -32.80)
>consensus
UAAAACGGUGGUCUAAAGGAGGCGGAGGACGCACAGUCCAGUUGCGUGUCCAAAUGGCGACGCACAGA_AAUGUGUGGAACCGUAAAGUGAGGGAACUUUUGUAGCAUUC___UUUUAAU
....((((.(((((...(((.(((.(((((.....))))...).))).)))..((((...((((((.....))))))...))))........)).))).))))................. (-29.06 = -29.00 +  -0.06)

alignment

secondary structure

dotplot

Window 4

Location	13,189,953 – 13,190,072
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.92
Mean single sequence MFE	-32.15
Consensus MFE	-25.90
Energy contribution	-25.52
Covariance contribution	-0.37
Combinations/Pair	1.18
Mean z-score	-1.59
Structure conservation index	0.81
SVM decision value	0.26
SVM RNA-class probability	0.657605
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13189953 119 + 22407834
GUUGCGCGUCCAAAUGGCGACGCACAGA-AAUGUUUGGAACCGUAAAGAGGUGGAACUUUUGUAGUAUUCUUCUUUUAAUAAUGCAUUAUAAUAGUGUCUGUCUGGAUGUGGACAAGUUC
(((.((((((((...(((((((((((((-(..((((...(((.......))).)))))))))).(((((.((.....)).))))).........))))).))))))))))))))...... ( -30.60)
>DroSec_CAF1 10348 115 + 1
GUUGCGUGUCCAAAUGGCGACGCACAGA-AAUGUGUGGAACCGUAAAGUGAGGGAACUUUUGUAGCAUUC---UUUUAAUAAUGCAUUAUAA-AAUGUCUGUCUGGAUGUGGACGAGUUU
(((.((..((((.((((...((((((..-..))))))...)))).....((.(((..((((((((((((.---.......)))))..)))))-))..))).))))))..)))))...... ( -34.80)
>DroSim_CAF1 10329 116 + 1
GUUGCGUGUCCAAAUGGCGACGCACAGA-AAUGUGUGGAACCGUAAAGUGAGGGAACUUUUGUAGCAUUC---UUUUAAUAAUGCAUUAUAAUAGUGUCUGUCUGGAUGUGGACGAGUUU
(((.((..((((.((((...((((((..-..))))))...)))).....((.((((((.((((((((((.---.......)))))..))))).))).))).))))))..)))))...... ( -35.10)
>DroYak_CAF1 10463 119 + 1
GUUGCGUGUCCAAUUGGCGACGCACAGAAAAUGUGUGGAACCAUAAAGUGAGGGAACUUUUGUAGUAUUCUUC-UUAAAUAAUGCAUUAUGAUGGUGUCUGUCUGGAUGUGAAGGAGUUG
....((..((((((.(((..((((((.....))))))..(((((.....(((((((((.....))).))))))-....((((....)))).)))))))).)).))))..))......... ( -28.10)
>consensus
GUUGCGUGUCCAAAUGGCGACGCACAGA_AAUGUGUGGAACCGUAAAGUGAGGGAACUUUUGUAGCAUUC___UUUUAAUAAUGCAUUAUAAUAGUGUCUGUCUGGAUGUGGACGAGUUU
(((.((((((((.((((...((((((.....))))))...)))).....((.((((((.((((((((((...........)))))..))))).))).))).)))))))))))))...... (-25.90 = -25.52 +  -0.37)

alignment

secondary structure

dotplot

Window 5

Location	13,189,992 – 13,190,112
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.38
Mean single sequence MFE	-30.90
Consensus MFE	-22.91
Energy contribution	-23.85
Covariance contribution	0.94
Combinations/Pair	1.11
Mean z-score	-1.75
Structure conservation index	0.74
SVM decision value	0.18
SVM RNA-class probability	0.620785
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13189992 120 + 22407834
CCGUAAAGAGGUGGAACUUUUGUAGUAUUCUUCUUUUAAUAAUGCAUUAUAAUAGUGUCUGUCUGGAUGUGGACAAGUUCCCACUUCUCCAACGACAGAUUUCCAUUCGCACGCAAUGAA
.(((...(((.(((((((.((((((((((.((.....)).)))))..))))).)))(((((((((((.((((........))))...))))..))))))).)))))))..)))....... ( -29.10)
>DroSec_CAF1 10387 116 + 1
CCGUAAAGUGAGGGAACUUUUGUAGCAUUC---UUUUAAUAAUGCAUUAUAA-AAUGUCUGUCUGGAUGUGGACGAGUUUCCACUUCUCCAACGACAGAUUUCCAUUCGCACGCAAUGAA
.......(((((((((.((((((((((((.---.......)))))..)))))-)).(((((((((((.(((((......)))))...))))..))))))))))).))))).......... ( -33.50)
>DroSim_CAF1 10368 117 + 1
CCGUAAAGUGAGGGAACUUUUGUAGCAUUC---UUUUAAUAAUGCAUUAUAAUAGUGUCUGUCUGGAUGUGGACGAGUUUCCACUUCUCCAACGACAGAUUUCCAUUCGCACGCAAUGAA
.......(((((((((((.((((((((((.---.......)))))..))))).)))(((((((((((.(((((......)))))...))))..))))))).))).))))).......... ( -34.20)
>DroYak_CAF1 10503 119 + 1
CCAUAAAGUGAGGGAACUUUUGUAGUAUUCUUC-UUAAAUAAUGCAUUAUGAUGGUGUCUGUCUGGAUGUGAAGGAGUUGCCUCUUCCCCAACGCCAGAUUUCCAUUCGCACGCAAUGAA
.(((.....(((((((((.....))).))))))-........(((.....(((((.....((((((...((..((((......))))..))...))))))..))))).....)))))).. ( -26.80)
>consensus
CCGUAAAGUGAGGGAACUUUUGUAGCAUUC___UUUUAAUAAUGCAUUAUAAUAGUGUCUGUCUGGAUGUGGACGAGUUUCCACUUCUCCAACGACAGAUUUCCAUUCGCACGCAAUGAA
.......(((((((((((.((((((((((...........)))))..))))).)))(((((((((((.((((........))))...))))..))))))).))).))))).......... (-22.91 = -23.85 +   0.94)

alignment

secondary structure

dotplot

Window 6

Location	13,190,032 – 13,190,142
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.84
Mean single sequence MFE	-30.17
Consensus MFE	-23.23
Energy contribution	-24.48
Covariance contribution	1.25
Combinations/Pair	1.00
Mean z-score	-1.88
Structure conservation index	0.77
SVM decision value	0.58
SVM RNA-class probability	0.789846
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13190032 110 + 22407834
AAUGCAUUAUAAUAGUGUCUGUCUGGAUGUGGACAAGUUCCCACUUCUCCAACGACAGAUUUCCAUUCGCACGCAAUGAAGAUUAAGAACUUUAAGGCAUGCAAGGAACU----------
................(((((((((((.((((........))))...))))..)))))))((((.((.(((.((..(((((........)))))..)).)))))))))..---------- ( -29.60)
>DroSec_CAF1 10424 109 + 1
AAUGCAUUAUAA-AAUGUCUGUCUGGAUGUGGACGAGUUUCCACUUCUCCAACGACAGAUUUCCAUUCGCACGCAAUGAAGAUUAAGAACUUUAAGGCAUGCAAGGAACU----------
............-...(((((((((((.(((((......)))))...))))..)))))))((((.((.(((.((..(((((........)))))..)).)))))))))..---------- ( -30.90)
>DroSim_CAF1 10405 110 + 1
AAUGCAUUAUAAUAGUGUCUGUCUGGAUGUGGACGAGUUUCCACUUCUCCAACGACAGAUUUCCAUUCGCACGCAAUGAAGAUUAAGAACUUUAAGGCAUGCAAGAAACU----------
..(((((.........(((((((((((.(((((......)))))...))))..)))))))............((..(((((........)))))..))))))).......---------- ( -28.80)
>DroYak_CAF1 10542 120 + 1
AAUGCAUUAUGAUGGUGUCUGUCUGGAUGUGAAGGAGUUGCCUCUUCCCCAACGCCAGAUUUCCAUUCGCACGCAAUGAAGAUUAAGAACUUUAGGGCAUGCUGGGAACUACAAUAUGUG
...((((..((.((((....((((((...((..((((......))))..))...))))))(((((...(((.((..(((((........)))))..)).))))))))))))))..)))). ( -31.40)
>consensus
AAUGCAUUAUAAUAGUGUCUGUCUGGAUGUGGACGAGUUUCCACUUCUCCAACGACAGAUUUCCAUUCGCACGCAAUGAAGAUUAAGAACUUUAAGGCAUGCAAGGAACU__________
................(((((((((((.((((........))))...))))..)))))))((((....(((.((..(((((........)))))..)).)))..))))............ (-23.23 = -24.48 +   1.25)

alignment

secondary structure

dotplot

Window 7

Location	13,190,032 – 13,190,142
Length	110
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.84
Mean single sequence MFE	-31.55
Consensus MFE	-27.04
Energy contribution	-27.60
Covariance contribution	0.56
Combinations/Pair	1.13
Mean z-score	-2.38
Structure conservation index	0.86
SVM decision value	1.72
SVM RNA-class probability	0.974130
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13190032 110 - 22407834
----------AGUUCCUUGCAUGCCUUAAAGUUCUUAAUCUUCAUUGCGUGCGAAUGGAAAUCUGUCGUUGGAGAAGUGGGAACUUGUCCACAUCCAGACAGACACUAUUAUAAUGCAUU
----------..((((((((((((..(.(((........))).)..))))))))..)))).((((((..((((...(((((......))))).))))))))))................. ( -32.10)
>DroSec_CAF1 10424 109 - 1
----------AGUUCCUUGCAUGCCUUAAAGUUCUUAAUCUUCAUUGCGUGCGAAUGGAAAUCUGUCGUUGGAGAAGUGGAAACUCGUCCACAUCCAGACAGACAUU-UUAUAAUGCAUU
----------..((((((((((((..(.(((........))).)..))))))))..)))).((((((..((((...(((((......))))).))))))))))((((-....)))).... ( -33.20)
>DroSim_CAF1 10405 110 - 1
----------AGUUUCUUGCAUGCCUUAAAGUUCUUAAUCUUCAUUGCGUGCGAAUGGAAAUCUGUCGUUGGAGAAGUGGAAACUCGUCCACAUCCAGACAGACACUAUUAUAAUGCAUU
----------.......(((((((..(.(((........))).)..)))))))(((((...((((((..((((...(((((......))))).))))))))))..))))).......... ( -30.80)
>DroYak_CAF1 10542 120 - 1
CACAUAUUGUAGUUCCCAGCAUGCCCUAAAGUUCUUAAUCUUCAUUGCGUGCGAAUGGAAAUCUGGCGUUGGGGAAGAGGCAACUCCUUCACAUCCAGACAGACACCAUCAUAAUGCAUU
.......((((.......((((((....(((........)))....))))))((.(((...((((...(((((((((((....)).))))...))))).))))..)))))....)))).. ( -30.10)
>consensus
__________AGUUCCUUGCAUGCCUUAAAGUUCUUAAUCUUCAUUGCGUGCGAAUGGAAAUCUGUCGUUGGAGAAGUGGAAACUCGUCCACAUCCAGACAGACACUAUUAUAAUGCAUU
............((((((((((((..(.(((........))).)..))))))))..)))).((((((..((((...(((((......))))).))))))))))................. (-27.04 = -27.60 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:29 2006