Locus 4410

Sequence ID	2R_DroMel_CAF1
Location	14,496,200 – 14,496,351
Length	151
Max. P	0.928032

overview

Window 8

Location	14,496,200 – 14,496,312
Length	112
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	81.26
Mean single sequence MFE	-33.38
Consensus MFE	-21.49
Energy contribution	-22.63
Covariance contribution	1.14
Combinations/Pair	1.18
Mean z-score	-2.71
Structure conservation index	0.64
SVM decision value	1.04
SVM RNA-class probability	0.904702
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14496200 112 + 20766785
AUAUUUAUGUAGUUUAUAUUUAUGCCAGUGCAUUCCGGCUUUUUUGCCCCU-UUCGGCAUUUGCCAACUUUAAUAUGUUGGCACAGCACGGAGGCACGGCUUUCGAUUCGCGU
(((..((((.....))))..)))(((.((((.((((((((....((((...-...))))..(((((((........))))))).))).))))))))))))............. ( -37.60)
>DroSec_CAF1 128287 108 + 1
AUAUUUAUUUAGUGCAUAUUUAUGCCAGUGCAUUCCGCCUUUUUUGCCCCUUUUCGGCAUUUGCCAACUUUAAUAUGUUGGCACAGCACGGAGGCACGGCUUUUGA-----GA
..................((((.(((.((((.(((((.......((((.......))))..(((((((........))))))).....))))))))))))...)))-----). ( -32.50)
>DroSim_CAF1 129419 112 + 1
AUAACCAUGAAGUGCAUAUUUAUGCCAGUGCAUUCCGCCUUUUUUGCCCCU-UUCGGCAUUUGCCAACUUUAAUAUGUUGGCACAGCACGGAGGCACGGCUUUCGAUUCGCGU
...........(((.((......(((.((((.(((((.......((((...-...))))..(((((((........))))))).....)))))))))))).....)).))).. ( -35.30)
>DroEre_CAF1 133560 111 + 1
AUACUUAUUUAGUGCAUAUUUAUGGCAGUGCAUGC-GCCUGUUUUCCCCCU-UUCGGCAUUUGCCAACUUUAAUAUGUUGGCACAGCACGAAGGCACGGCUUUCGAUUCGCGU
.((((.....))))..........((.((((....-(((............-...)))...(((((((........)))))))..))))((((((...)))))).....)).. ( -29.66)
>DroYak_CAF1 131706 108 + 1
---UCUGUUUAGUGCAUAUUUAUGGCAGUGCAUUC-GGCUGUUUUCCCCCU-UUCGGCAUUUGCCAACUUUAAUAUGUUGGCACAGCACGGAGGCACGGCUUUCGAUUCGCGU
---..........((..(((...(((.((((.(((-((((((......((.-...)).....((((((........))))))))))).)))).)))).)))...)))..)).. ( -34.60)
>DroAna_CAF1 141209 100 + 1
AAUUUUUUGUAAU---AAUUUAGUCC--UGCCCUCCUGCC--GUUGCCCCU-UUCGGCAGUCGCUAACUUUAAUAUGUUGGCACAGCUCGAAGGCGCGGGCUUC-----CUCU
.............---.....(((((--((((.(((((((--(........-..))))))..((((((........)))))).......)).)))).)))))..-----.... ( -30.60)
>consensus
AUAUUUAUGUAGUGCAUAUUUAUGCCAGUGCAUUCCGCCUUUUUUGCCCCU_UUCGGCAUUUGCCAACUUUAAUAUGUUGGCACAGCACGGAGGCACGGCUUUCGAUUCGCGU
.......................(((.((((.(((((.......((((.......))))...((((((........))))))......))))))))))))............. (-21.49 = -22.63 +   1.14)

alignment

secondary structure

dotplot

Window 9

Location	14,496,200 – 14,496,312
Length	112
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	81.26
Mean single sequence MFE	-33.75
Consensus MFE	-19.91
Energy contribution	-20.22
Covariance contribution	0.31
Combinations/Pair	1.20
Mean z-score	-3.11
Structure conservation index	0.59
SVM decision value	1.19
SVM RNA-class probability	0.928032
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14496200 112 - 20766785
ACGCGAAUCGAAAGCCGUGCCUCCGUGCUGUGCCAACAUAUUAAAGUUGGCAAAUGCCGAA-AGGGGCAAAAAAGCCGGAAUGCACUGGCAUAAAUAUAAACUACAUAAAUAU
.............(((((((.((((.(((.(((((((........)))))))..((((...-...))))....)))))))..)))).)))....................... ( -36.90)
>DroSec_CAF1 128287 108 - 1
UC-----UCAAAAGCCGUGCCUCCGUGCUGUGCCAACAUAUUAAAGUUGGCAAAUGCCGAAAAGGGGCAAAAAAGGCGGAAUGCACUGGCAUAAAUAUGCACUAAAUAAAUAU
..-----......(((((((.(((((....(((((((........)))))))..((((.......))))......)))))..)))).)))....................... ( -34.00)
>DroSim_CAF1 129419 112 - 1
ACGCGAAUCGAAAGCCGUGCCUCCGUGCUGUGCCAACAUAUUAAAGUUGGCAAAUGCCGAA-AGGGGCAAAAAAGGCGGAAUGCACUGGCAUAAAUAUGCACUUCAUGGUUAU
............((((((((.(((((....(((((((........)))))))..((((...-...))))......)))))..))))..((((....)))).......)))).. ( -36.00)
>DroEre_CAF1 133560 111 - 1
ACGCGAAUCGAAAGCCGUGCCUUCGUGCUGUGCCAACAUAUUAAAGUUGGCAAAUGCCGAA-AGGGGGAAAACAGGC-GCAUGCACUGCCAUAAAUAUGCACUAAAUAAGUAU
..(((........((.((((....(((((.(((((((........)))))))..(.((...-.)).).......)))-))..)))).))........)))............. ( -30.99)
>DroYak_CAF1 131706 108 - 1
ACGCGAAUCGAAAGCCGUGCCUCCGUGCUGUGCCAACAUAUUAAAGUUGGCAAAUGCCGAA-AGGGGGAAAACAGCC-GAAUGCACUGCCAUAAAUAUGCACUAAACAGA---
..(((........((.((((...((.(((((((((((........))))))...(.((...-.)).)....))))))-)...)))).))........)))..........--- ( -33.39)
>DroAna_CAF1 141209 100 - 1
AGAG-----GAAGCCCGCGCCUUCGAGCUGUGCCAACAUAUUAAAGUUAGCGACUGCCGAA-AGGGGCAAC--GGCAGGAGGGCA--GGACUAAAUU---AUUACAAAAAAUU
....-----..((.((..((((((..((((((((..........((((...)))).((...-.))))).))--)))..)))))).--)).)).....---............. ( -31.20)
>consensus
ACGCGAAUCGAAAGCCGUGCCUCCGUGCUGUGCCAACAUAUUAAAGUUGGCAAAUGCCGAA_AGGGGCAAAAAAGCCGGAAUGCACUGGCAUAAAUAUGCACUAAAUAAAUAU
................((.(((.((.((..(((((((........)))))))...))))...))).))............((((....))))..................... (-19.91 = -20.22 +   0.31)

alignment

secondary structure

dotplot

Window 0

Location	14,496,238 – 14,496,351
Length	113
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	83.87
Mean single sequence MFE	-35.95
Consensus MFE	-22.80
Energy contribution	-23.53
Covariance contribution	0.73
Combinations/Pair	1.14
Mean z-score	-2.32
Structure conservation index	0.63
SVM decision value	-0.05
SVM RNA-class probability	0.506987
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14496238 113 - 20766785
UUCAACAUCCGGCUUCCGCUGCAAUGUAAUGGAAACUCGACGCGAAUCGAAAGCCGUGCCUCCGUGCUGUGCCAACAUAUUAAAGUUGGCAAAUGCCGAA-AGGGGCAAAAA-AG
.........((((((.((.(((...((...(....)...)))))...)).))))))((((((((.((..(((((((........)))))))...))))..-.))))))....-.. ( -37.30)
>DroPse_CAF1 127641 109 - 1
UUCAACAUCCGGCUUCCGUUGCAGUGUAAUGGAAACUCAAGGCGA-----GUGCCGUGCCGCCAUGCUGUGCCAACAUAUUAAAGUUGGCAAAUGCCGAA-AGCACCAGAACCAG
(((.......((((((((((((...)))))))))((((.....))-----)))))((((((.(((....(((((((........))))))).))).))..-.))))..))).... ( -35.70)
>DroSec_CAF1 128325 109 - 1
UUCAACAUCCGGCUUCCGCUGCAAUGUAAUGGAAACUCGUC-----UCAAAAGCCGUGCCUCCGUGCUGUGCCAACAUAUUAAAGUUGGCAAAUGCCGAAAAGGGGCAAAAA-AG
.........((((((....((..(((....(....).))).-----.)).))))))((((((((.((..(((((((........)))))))...))))....))))))....-.. ( -32.90)
>DroEre_CAF1 133597 113 - 1
UUCAACAUCCGGCUUCCGUUGCAAUGUAAUGGAAACUCGACGCGAAUCGAAAGCCGUGCCUUCGUGCUGUGCCAACAUAUUAAAGUUGGCAAAUGCCGAA-AGGGGGAAAAC-AG
.......(((((((((((((((...)))))))))..((((......))))..)))...((((((.((..(((((((........)))))))...)))).)-))).)))....-.. ( -40.10)
>DroAna_CAF1 141242 106 - 1
UUCAACAUCCGGCUUCCGCUACAAUGUAAUGGAAACUCAAGAG-----GAAGCCCGCGCCUUCGAGCUGUGCCAACAUAUUAAAGUUAGCGACUGCCGAA-AGGGGCAAC---GG
........(((((((((((......))...(....)......)-----)))))).((.((((((.((..(((.(((........))).)))...)))).)-))).))...---)) ( -34.00)
>DroPer_CAF1 129799 109 - 1
UUCAACAUCCGGCUUCCGUUGCAGUGUAAUGGAAACUCAAGGCGA-----GUGCCGUGCCGCCAUGCUGUGCCAACAUAUUAAAGUUGGCAAAUGCCGAA-AGCACCAGAACCAG
(((.......((((((((((((...)))))))))((((.....))-----)))))((((((.(((....(((((((........))))))).))).))..-.))))..))).... ( -35.70)
>consensus
UUCAACAUCCGGCUUCCGCUGCAAUGUAAUGGAAACUCAACGCGA___GAAAGCCGUGCCUCCGUGCUGUGCCAACAUAUUAAAGUUGGCAAAUGCCGAA_AGGGGCAAAAC_AG
.........(((((((((.(((...))).)))))..................))))((((((((.((..(((((((........)))))))...))))....))))))....... (-22.80 = -23.53 +   0.73)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:57 2006