Locus 6143

Sequence ID	2L_DroMel_CAF1
Location	17,136,971 – 17,137,207
Length	236
Max. P	0.875888

overview

Window 0

Location	17,136,971 – 17,137,090
Length	119
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	98.32
Mean single sequence MFE	-31.49
Consensus MFE	-30.48
Energy contribution	-30.68
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.34
Structure conservation index	0.97
SVM decision value	0.70
SVM RNA-class probability	0.827016
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17136971 119 + 22407834
UAACUUUGAUGUCGCCGAAAGUCUCUUUGCUCUCUUUUAUUUAUUACACGCCCGCAGAUGCCCCGUUUCGUUAUAUUCGGUGGAAAAUGGGCGAACUACUUUUCGGCUUUUGGCGUUGU
............(((((((((((..........................(((((......(((((............))).))....)))))(((......)))))))))))))).... ( -31.00)
>DroSec_CAF1 105335 118 + 1
UAACUUUGAUGUCGCCGAAAGUCUCUUUGCUCUCUUUUAUGUAAUA-ACGCCCUCAGAUGCCCCGUUUCGUUAUAUUCGGUGGAAAAUGGGCGAACUACUUUUCGGCUUUUGGCGUUGU
............(((((((((((...((((..........))))..-.(((((.......(((((............))).)).....)))))...........))))))))))).... ( -32.90)
>DroSim_CAF1 117551 119 + 1
UAACUUUGAUGUCGCCGAAAGUCUCUUUGCUCUCUUUUAUUUAUUACACGCCCGCAGAUGCCCCGUUUCGUUAUAUUCGGUGGAAAAUGGGCGAACUACUUUUCGGCUUUUGGCGUUGU
............(((((((((((..........................(((((......(((((............))).))....)))))(((......)))))))))))))).... ( -31.00)
>DroEre_CAF1 102897 119 + 1
UAACUUUGAUGUCGCCGAAAGUCUCUGUGCUCUCUUUUAUUUAUUACACGCCCGCAGAUGCCCCGUUUCGUUAUAUUCGGUGGAAAAUGGGCGAACUACUUUUCGGCUUUUGGCGUUGU
............(((((((((((..((((...............))))((((((......(((((............))).))....))))))...........))))))))))).... ( -31.56)
>DroYak_CAF1 105396 119 + 1
UAACUUUGAUGUCGCCGAAAGUCUCUUUGCUCUCUUUUAUUUAUUACACGCCCGCAGAUGCCCCGUUUCGUUAUAUUCGGUGGAAAAUGGGCGAACUACUUUUCGGCUUUUGGCGUUGU
............(((((((((((..........................(((((......(((((............))).))....)))))(((......)))))))))))))).... ( -31.00)
>consensus
UAACUUUGAUGUCGCCGAAAGUCUCUUUGCUCUCUUUUAUUUAUUACACGCCCGCAGAUGCCCCGUUUCGUUAUAUUCGGUGGAAAAUGGGCGAACUACUUUUCGGCUUUUGGCGUUGU
............(((((((((((..........................(((((......(((((............))).))....)))))(((......)))))))))))))).... (-30.48 = -30.68 +   0.20)

alignment

secondary structure

dotplot

Window 1

Location	17,136,971 – 17,137,090
Length	119
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	98.32
Mean single sequence MFE	-28.36
Consensus MFE	-27.34
Energy contribution	-27.54
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.40
Structure conservation index	0.96
SVM decision value	0.89
SVM RNA-class probability	0.875888
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17136971 119 - 22407834
ACAACGCCAAAAGCCGAAAAGUAGUUCGCCCAUUUUCCACCGAAUAUAACGAAACGGGGCAUCUGCGGGCGUGUAAUAAAUAAAAGAGAGCAAAGAGACUUUCGGCGACAUCAAAGUUA
....((((....(((.....((((...((((..((((.............))))..))))..)))).)))...............(((((........)))))))))............ ( -28.22)
>DroSec_CAF1 105335 118 - 1
ACAACGCCAAAAGCCGAAAAGUAGUUCGCCCAUUUUCCACCGAAUAUAACGAAACGGGGCAUCUGAGGGCGU-UAUUACAUAAAAGAGAGCAAAGAGACUUUCGGCGACAUCAAAGUUA
....((((............(((((.(((((.....((.(((............))))).......))))).-.)))))......(((((........)))))))))............ ( -28.90)
>DroSim_CAF1 117551 119 - 1
ACAACGCCAAAAGCCGAAAAGUAGUUCGCCCAUUUUCCACCGAAUAUAACGAAACGGGGCAUCUGCGGGCGUGUAAUAAAUAAAAGAGAGCAAAGAGACUUUCGGCGACAUCAAAGUUA
....((((....(((.....((((...((((..((((.............))))..))))..)))).)))...............(((((........)))))))))............ ( -28.22)
>DroEre_CAF1 102897 119 - 1
ACAACGCCAAAAGCCGAAAAGUAGUUCGCCCAUUUUCCACCGAAUAUAACGAAACGGGGCAUCUGCGGGCGUGUAAUAAAUAAAAGAGAGCACAGAGACUUUCGGCGACAUCAAAGUUA
....((((....(((.....((((...((((..((((.............))))..))))..)))).)))...............(((((........)))))))))............ ( -28.22)
>DroYak_CAF1 105396 119 - 1
ACAACGCCAAAAGCCGAAAAGUAGUUCGCCCAUUUUCCACCGAAUAUAACGAAACGGGGCAUCUGCGGGCGUGUAAUAAAUAAAAGAGAGCAAAGAGACUUUCGGCGACAUCAAAGUUA
....((((....(((.....((((...((((..((((.............))))..))))..)))).)))...............(((((........)))))))))............ ( -28.22)
>consensus
ACAACGCCAAAAGCCGAAAAGUAGUUCGCCCAUUUUCCACCGAAUAUAACGAAACGGGGCAUCUGCGGGCGUGUAAUAAAUAAAAGAGAGCAAAGAGACUUUCGGCGACAUCAAAGUUA
....((((....(((.....((((...((((..((((.............))))..))))..)))).)))...............(((((........)))))))))............ (-27.34 = -27.54 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	17,137,090 – 17,137,207
Length	117
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	99.32
Mean single sequence MFE	-20.50
Consensus MFE	-20.50
Energy contribution	-20.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.23
Structure conservation index	1.00
SVM decision value	0.17
SVM RNA-class probability	0.616488
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17137090 117 + 22407834
UAACAUUUCAUUUCUGCCGCAUUUCAUUUCGCCUGCGAUGCGUUUUAUGAAUUCAGUUAUUCCGUUGGCUGCAUAUUCAAUUU-UUUAUUCGCUUUCCCACCGCAGCUUGGCAUCUCC
.......(((...((((((((((.((.......)).)))))).....(((((.((((((......))))))...)))))....-..................))))..)))....... ( -20.50)
>DroSec_CAF1 105453 117 + 1
UAACAUUUCAUUUCUGCCGCAUUUCAUUUCGCCUGCGAUGCGUUUUAUGAAUUCAGUUAUUCCGUUGGCUGCAUAUUCAAUUU-UUUAUUCGCUUUCCCACCGCAGCUUGGCAUCUCC
.......(((...((((((((((.((.......)).)))))).....(((((.((((((......))))))...)))))....-..................))))..)))....... ( -20.50)
>DroSim_CAF1 117670 117 + 1
UAACAUUUCAUUUCUGCCGCAUUUCAUUUCGCCUGCGAUGCGUUUUAUGAAUUCAGUUAUUCCGUUGGCUGCAUAUUCAAUUU-UUUAUUCGCUUUCCCACCGCAGCUUGGCAUCUCC
.......(((...((((((((((.((.......)).)))))).....(((((.((((((......))))))...)))))....-..................))))..)))....... ( -20.50)
>DroEre_CAF1 103016 117 + 1
UAACAUUUCAUUUCUGCCGCAUUUCAUUUCGCCUGCGAUGCGUUUUAUGAAUUCAGUUAUUCCGUUGGCUGCAUAUUCAAUUU-UUUAUUCGCUUUCCCACCGCAGCUUGGCAUCUCC
.......(((...((((((((((.((.......)).)))))).....(((((.((((((......))))))...)))))....-..................))))..)))....... ( -20.50)
>DroYak_CAF1 105515 118 + 1
UAACAUUUCAUUUCUGCCGCAUUUCAUUUCGCCUGCGAUGCGUUUUAUGAAUUCAGUUAUUCCGUUGGCUGCAUAUUCAAUUUUUUUAUUCGCUUUCCCACCGCAGCUUGGCAUUUCC
.......(((...((((((((((.((.......)).)))))).....(((((.((((((......))))))...))))).......................))))..)))....... ( -20.50)
>consensus
UAACAUUUCAUUUCUGCCGCAUUUCAUUUCGCCUGCGAUGCGUUUUAUGAAUUCAGUUAUUCCGUUGGCUGCAUAUUCAAUUU_UUUAUUCGCUUUCCCACCGCAGCUUGGCAUCUCC
.......(((...((((((((((.((.......)).)))))).....(((((.((((((......))))))...))))).......................))))..)))....... (-20.50 = -20.50 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	17,137,090 – 17,137,207
Length	117
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	99.32
Mean single sequence MFE	-24.08
Consensus MFE	-24.00
Energy contribution	-24.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.34
Structure conservation index	1.00
SVM decision value	0.53
SVM RNA-class probability	0.771206
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17137090 117 - 22407834
GGAGAUGCCAAGCUGCGGUGGGAAAGCGAAUAAA-AAAUUGAAUAUGCAGCCAACGGAAUAACUGAAUUCAUAAAACGCAUCGCAGGCGAAAUGAAAUGCGGCAGAAAUGAAAUGUUA
.....((((...((((((((((...(((.((...-.......)).)))..))....((((......))))........))))))))(((........))))))).............. ( -24.10)
>DroSec_CAF1 105453 117 - 1
GGAGAUGCCAAGCUGCGGUGGGAAAGCGAAUAAA-AAAUUGAAUAUGCAGCCAACGGAAUAACUGAAUUCAUAAAACGCAUCGCAGGCGAAAUGAAAUGCGGCAGAAAUGAAAUGUUA
.....((((...((((((((((...(((.((...-.......)).)))..))....((((......))))........))))))))(((........))))))).............. ( -24.10)
>DroSim_CAF1 117670 117 - 1
GGAGAUGCCAAGCUGCGGUGGGAAAGCGAAUAAA-AAAUUGAAUAUGCAGCCAACGGAAUAACUGAAUUCAUAAAACGCAUCGCAGGCGAAAUGAAAUGCGGCAGAAAUGAAAUGUUA
.....((((...((((((((((...(((.((...-.......)).)))..))....((((......))))........))))))))(((........))))))).............. ( -24.10)
>DroEre_CAF1 103016 117 - 1
GGAGAUGCCAAGCUGCGGUGGGAAAGCGAAUAAA-AAAUUGAAUAUGCAGCCAACGGAAUAACUGAAUUCAUAAAACGCAUCGCAGGCGAAAUGAAAUGCGGCAGAAAUGAAAUGUUA
.....((((...((((((((((...(((.((...-.......)).)))..))....((((......))))........))))))))(((........))))))).............. ( -24.10)
>DroYak_CAF1 105515 118 - 1
GGAAAUGCCAAGCUGCGGUGGGAAAGCGAAUAAAAAAAUUGAAUAUGCAGCCAACGGAAUAACUGAAUUCAUAAAACGCAUCGCAGGCGAAAUGAAAUGCGGCAGAAAUGAAAUGUUA
.....((((...((((((((((...(((.((...........)).)))..))....((((......))))........))))))))(((........))))))).............. ( -24.00)
>consensus
GGAGAUGCCAAGCUGCGGUGGGAAAGCGAAUAAA_AAAUUGAAUAUGCAGCCAACGGAAUAACUGAAUUCAUAAAACGCAUCGCAGGCGAAAUGAAAUGCGGCAGAAAUGAAAUGUUA
.....((((...((((((((((...(((.((...........)).)))..))....((((......))))........))))))))(((........))))))).............. (-24.00 = -24.00 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:29 2006