Locus 5035

Sequence ID	X_DroMel_CAF1
Location	13,178,138 – 13,178,293
Length	155
Max. P	0.996463

overview

Window 4

Location	13,178,138 – 13,178,254
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.94
Mean single sequence MFE	-26.82
Consensus MFE	-23.16
Energy contribution	-23.20
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.32
Structure conservation index	0.86
SVM decision value	-0.05
SVM RNA-class probability	0.507831
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13178138 116 - 22224390
CCCAACAUGUUUGCAUUUAAUUAAUGCGUACACAUGGCUUAAAAGCUGAUUAUCCUUAAUUAGUGUUGUCUUUGGCCACACAUUUUACCUGAGAGCAUUUGG----CGUAGGCUAGAUUU
.....(((((.((((((.....))))))...)))))((((....((((((((....))))))))((.((.....)).)).............))))((((((----(....))))))).. ( -27.40)
>DroSec_CAF1 8087 116 - 1
CCCAACAUGUUUGCAUUUAAUUAAUGCGUACACAUGGCUUAAAAGCUGAUUAUCCUUAAUUAGUGUUGUCUUUGGCCACACAUUUUACCUGAGAGCAUUUGA----CGUAGACUAGAUUU
.....(((((.((((((.....))))))...)))))(((((((.((((((((....))))).((((.((.....)).))))............))).)))))----.))........... ( -22.30)
>DroSim_CAF1 8209 116 - 1
CCCAACAUGUUUGCAUUUAAUUAAUGCGUACACAUGGCUUAAAAGCUGAUUAUCCUUAAUUAGUGUUGUCUUUGGCCACACAUUUUACCUGAGAGCAUUUGG----CGUAGGCUAGAUUU
.....(((((.((((((.....))))))...)))))((((....((((((((....))))))))((.((.....)).)).............))))((((((----(....))))))).. ( -27.40)
>DroEre_CAF1 12063 120 - 1
CCCAACAUGUUUGUAUUUAAUUAAUGCGUACACAUGGCUUAAAAGCUGAUUAUCCUUAAUUAGUGUUGUCUUUGGCCACACAUUUUACCUGAGAGCAUUUGGCCCUCGUAGGCUAGAUUU
.....(((((.((((((.....))))))...)))))((((....((((((((....))))))))((.((.....)).)).............))))((((((((......)))))))).. ( -28.30)
>DroYak_CAF1 13819 116 - 1
CCCAACAUGUUUGCAUUUAAUUAAUGCGUACACAUGGCUUAAAAGCUGAUUAUCCUUAAUUAGUGUUGUCUUUGGCCACACAUUCUACCUGAGAGCAUUCGG----CGUAGGCUAGAUUU
.....(((((.((((((.....))))))...)))))(((((...(((((.............((((.((.....)).)))).((((.....))))...))))----).)))))....... ( -28.70)
>consensus
CCCAACAUGUUUGCAUUUAAUUAAUGCGUACACAUGGCUUAAAAGCUGAUUAUCCUUAAUUAGUGUUGUCUUUGGCCACACAUUUUACCUGAGAGCAUUUGG____CGUAGGCUAGAUUU
.....(((((.((((((.....))))))...)))))(((((...((((((((....))))))))(((.((...((............)).)).)))............)))))....... (-23.16 = -23.20 +   0.04)

alignment

secondary structure

dotplot

Window 5

Location	13,178,174 – 13,178,293
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.56
Mean single sequence MFE	-18.36
Consensus MFE	-17.08
Energy contribution	-17.28
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.21
Structure conservation index	0.93
SVM decision value	0.48
SVM RNA-class probability	0.751815
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13178174 119 + 22224390
UGUGGCCAAAGACAACACUAAUUAAGGAUAAUCAGCUUUUAAGCCAUGUGUACGCAUUAAUUAAAUGCAAACAUGUUGGGUAAA-AGGAAACAAGGAAACAAAAAGAAAAAAAAAGAUGU
(((..((..........((.((((....)))).))((((((..((((((((..(((((.....)))))..))))).))).))))-)).......))..)))................... ( -19.20)
>DroSec_CAF1 8123 118 + 1
UGUGGCCAAAGACAACACUAAUUAAGGAUAAUCAGCUUUUAAGCCAUGUGUACGCAUUAAUUAAAUGCAAACAUGUUGGGUAAA-AGGAAACAAGGAAACAAAACAAAAA-AAAAUAUGU
(((..((..........((.((((....)))).))((((((..((((((((..(((((.....)))))..))))).))).))))-)).......))..))).........-......... ( -19.20)
>DroSim_CAF1 8245 119 + 1
UGUGGCCAAAGACAACACUAAUUAAGGAUAAUCAGCUUUUAAGCCAUGUGUACGCAUUAAUUAAAUGCAAACAUGUUGGGUAAA-AGGAAACAAGGAAACAAAACAAAAAAAAAAGAUGU
(((..((..........((.((((....)))).))((((((..((((((((..(((((.....)))))..))))).))).))))-)).......))..)))................... ( -19.20)
>DroEre_CAF1 12103 109 + 1
UGUGGCCAAAGACAACACUAAUUAAGGAUAAUCAGCUUUUAAGCCAUGUGUACGCAUUAAUUAAAUACAAACAUGUUGGGAAAG--GGAAACAAGGAAACAA---------AAAAGAUGU
(((..((.....(((((((.....))........(..(((((...((((....))))...)))))..).....)))))......--))..))).(....)..---------......... ( -14.90)
>DroYak_CAF1 13855 111 + 1
UGUGGCCAAAGACAACACUAAUUAAGGAUAAUCAGCUUUUAAGCCAUGUGUACGCAUUAAUUAAAUGCAAACAUGUUGGGAAAAGAGGAAACCAGGAAACAA---------AAAAGAUGU
(((..((..((......))......((....((..(((((...((((((((..(((((.....)))))..))))).))).)))))..))..)).))..))).---------......... ( -19.30)
>consensus
UGUGGCCAAAGACAACACUAAUUAAGGAUAAUCAGCUUUUAAGCCAUGUGUACGCAUUAAUUAAAUGCAAACAUGUUGGGUAAA_AGGAAACAAGGAAACAAAA__AAAA_AAAAGAUGU
(((..((.....((((..................(((....)))...((((..(((((.....)))))..))))))))........(....)..))..)))................... (-17.08 = -17.28 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	13,178,174 – 13,178,293
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.56
Mean single sequence MFE	-19.13
Consensus MFE	-19.20
Energy contribution	-19.04
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-1.66
Structure conservation index	1.00
SVM decision value	2.70
SVM RNA-class probability	0.996463
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13178174 119 - 22224390
ACAUCUUUUUUUUUCUUUUUGUUUCCUUGUUUCCU-UUUACCCAACAUGUUUGCAUUUAAUUAAUGCGUACACAUGGCUUAAAAGCUGAUUAUCCUUAAUUAGUGUUGUCUUUGGCCACA
...................................-...........(((.((((((.....)))))).)))..(((((.....((((((((....)))))))).........))))).. ( -19.44)
>DroSec_CAF1 8123 118 - 1
ACAUAUUUU-UUUUUGUUUUGUUUCCUUGUUUCCU-UUUACCCAACAUGUUUGCAUUUAAUUAAUGCGUACACAUGGCUUAAAAGCUGAUUAUCCUUAAUUAGUGUUGUCUUUGGCCACA
.........-.........................-...........(((.((((((.....)))))).)))..(((((.....((((((((....)))))))).........))))).. ( -19.44)
>DroSim_CAF1 8245 119 - 1
ACAUCUUUUUUUUUUGUUUUGUUUCCUUGUUUCCU-UUUACCCAACAUGUUUGCAUUUAAUUAAUGCGUACACAUGGCUUAAAAGCUGAUUAUCCUUAAUUAGUGUUGUCUUUGGCCACA
...................................-...........(((.((((((.....)))))).)))..(((((.....((((((((....)))))))).........))))).. ( -19.44)
>DroEre_CAF1 12103 109 - 1
ACAUCUUUU---------UUGUUUCCUUGUUUCC--CUUUCCCAACAUGUUUGUAUUUAAUUAAUGCGUACACAUGGCUUAAAAGCUGAUUAUCCUUAAUUAGUGUUGUCUUUGGCCACA
.........---------................--...........(((.((((((.....)))))).)))..(((((.....((((((((....)))))))).........))))).. ( -17.44)
>DroYak_CAF1 13855 111 - 1
ACAUCUUUU---------UUGUUUCCUGGUUUCCUCUUUUCCCAACAUGUUUGCAUUUAAUUAAUGCGUACACAUGGCUUAAAAGCUGAUUAUCCUUAAUUAGUGUUGUCUUUGGCCACA
.........---------........(((((..............(((((.((((((.....))))))...)))))........((((((((....)))))))).........))))).. ( -19.90)
>consensus
ACAUCUUUU_UUUU__UUUUGUUUCCUUGUUUCCU_UUUACCCAACAUGUUUGCAUUUAAUUAAUGCGUACACAUGGCUUAAAAGCUGAUUAUCCUUAAUUAGUGUUGUCUUUGGCCACA
...............................................(((.((((((.....)))))).)))..(((((.....((((((((....)))))))).........))))).. (-19.20 = -19.04 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:38 2006