Locus 2498

Sequence ID	3R_DroMel_CAF1
Location	6,829,326 – 6,829,523
Length	197
Max. P	0.651176

overview

Window 5

Location	6,829,326 – 6,829,418
Length	92
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.72
Mean single sequence MFE	-25.43
Consensus MFE	-16.49
Energy contribution	-16.52
Covariance contribution	0.03
Combinations/Pair	1.21
Mean z-score	-1.60
Structure conservation index	0.65
SVM decision value	0.22
SVM RNA-class probability	0.640669
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6829326 92 + 27905053
---------------------------CGACCACUGCCAAAAUUGGCGGUCAAUUAAAACGGCGGCCUGAUUGAAAUUCAUUUUCGGUCGAAAACCAAAUGGGCGU-UGAAAAAUAUGCU
---------------------------.((((...((((....))))))))........(((((.((.((((((((.....))))))))(.....)....)).)))-))........... ( -25.60)
>DroSec_CAF1 88411 92 + 1
---------------------------CGACCACUGCCAAAAUUGGUGGUCAAUUAAAACGGCGGCCUGACUGAAAUUCAUUUUAGGUCGAAAACCAACUGGGAGU-UGAAAAAUAUGCU
---------------------------.(((((((.........))))))).........((((((((((.((.....))..)))))))......((((.....))-))........))) ( -24.30)
>DroSim_CAF1 94685 119 + 1
NNNNNNNNNNNNGGUGGAUUCAACUUUCGACCACUGCCAAAAUUGGCGGUCAAUUAAAACGGCGGCCUGAUUGAAAUUCAUUUUAGGUCGAAAACCAACUGGGCGU-UGAAAAAUAUGCU
..................((((((((((((((.((((((....))))))(((((((...........)))))))...........)))))))).((....))..))-))))......... ( -30.80)
>DroEre_CAF1 73376 92 + 1
---------------------------CGACCACUGCCGAAAUUGGUGGUCAAUUAAAACGGUGGCCUGAUUGAAAUUCAUUUUAGGUCGAAAACCAACUGGGCGU-UGAAAAAUAUGCU
---------------------------.(((((((.........))))))).........((((((((((.((.....))..)))))))....))).....(((((-........))))) ( -25.00)
>DroYak_CAF1 86736 92 + 1
---------------------------CGACCACUGCCGAAAUUGGCGGUCAAUUAAAACGGUGGCCUGAUUGAAAUUCAUUUUAGGGCGAAAACCAACUGGGCGU-UGAAAAAUAUGCU
---------------------------...(((((((((....)))))))..........((((.(((((.((.....))..))))).)....)))....))((((-........)))). ( -22.30)
>DroAna_CAF1 44662 93 + 1
---------------------------UGGCUACUGUCGAAAUUGGCGGUCAAUUAAAAUGGCGGCCUGAUUGAAAUUUCAUUUGUACGGAAUGUGGACGGGGCGUAUGAGUAAUAUGCU
---------------------------......(((((..(((((((.((((.......)))).))).))))...(((((........)))))...)))))(((((((.....))))))) ( -24.60)
>consensus
___________________________CGACCACUGCCAAAAUUGGCGGUCAAUUAAAACGGCGGCCUGAUUGAAAUUCAUUUUAGGUCGAAAACCAACUGGGCGU_UGAAAAAUAUGCU
...........................(((((.((((((....))))))(((((((...........)))))))...........)))))...........(((((.(.....).))))) (-16.49 = -16.52 +   0.03)

alignment

secondary structure

dotplot

Window 6

Location	6,829,379 – 6,829,483
Length	104
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	84.36
Mean single sequence MFE	-20.54
Consensus MFE	-13.30
Energy contribution	-13.54
Covariance contribution	0.24
Combinations/Pair	1.10
Mean z-score	-1.83
Structure conservation index	0.65
SVM decision value	0.06
SVM RNA-class probability	0.565011
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6829379 104 - 27905053
UGGUUGCCAAAGAAAAAUGGCAAA---ACAAAA-AAUGAAAAGAACAGGAGCCAGCUUCAAAAGCAGUAAGCAUAUUUUUCAACGCCCAUUUGGUUUUCGACCGAAAA
(((((((((........)))))).---......-..(((((((....((((....))))....((.....))...)))))))....)))(((((((...))))))).. ( -22.80)
>DroSec_CAF1 88464 99 - 1
UGGUUGCCAAAGAAAAAUGGCAAACAAACAAAAAAAA---------AUGAGCCAGCUUCAAAAGCAGUAAGCAUAUUUUUCAACUCCCAGUUGGUUUUCGACCUAAAA
.((((((((........))))....((((....((((---------(((.((..(((.(....).)))..)).)))))))((((.....))))))))..))))..... ( -18.20)
>DroSim_CAF1 94765 108 - 1
UGGUUGCCAAAGAAAAAUGGCAAACAAACAAAAAAAAAAAAAGAAAAGGGGCCAGCUUUAAAAGCAGUAAGCAUAUUUUUCAACGCCCAGUUGGUUUUCGACCUAAAA
.((((((((........)))).................((((..((..((((..(((.....))).(....)............))))..))..)))).))))..... ( -18.90)
>DroEre_CAF1 73429 102 - 1
UGGUUGCCAAAGAAAAAUUGGGAACAA------AAAUAAAAAGAACAGGGGCCAGCUUCAAAAGCAGUAAGCAUAUUUUUCAACGCCCAGUUGGUUUUCGACCUAAAA
.(((((...((((..(((((((...((------(((((.........((((....))))....((.....)).))))))).....)))))))..)))))))))..... ( -22.70)
>DroYak_CAF1 86789 100 - 1
UGGUUGCCAAAGAAAAAUG--GCAAAA------AAAAAAACAGAGCAGGGGUCAGCUUCAAAAGCAGUAAGCAUAUUUUUCAACGCCCAGUUGGUUUUCGCCCUAAAA
...((((((........))--))))..------..............(((((..(((((.......).)))).......(((((.....))))).....))))).... ( -20.10)
>consensus
UGGUUGCCAAAGAAAAAUGGCAAACAAACAAAAAAAAAAAAAGAACAGGGGCCAGCUUCAAAAGCAGUAAGCAUAUUUUUCAACGCCCAGUUGGUUUUCGACCUAAAA
.(((((.....((((((((............................((((....))))....((.....)).)))))))).....((....))....)))))..... (-13.30 = -13.54 +   0.24)

alignment

secondary structure

dotplot

Window 7

Location	6,829,418 – 6,829,523
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.97
Mean single sequence MFE	-24.86
Consensus MFE	-13.52
Energy contribution	-13.17
Covariance contribution	-0.36
Combinations/Pair	1.38
Mean z-score	-1.81
Structure conservation index	0.54
SVM decision value	0.25
SVM RNA-class probability	0.651176
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6829418 105 + 27905053
UACUGCUUUUGAAGCUGGCUCCUGUUCUUUUCAUU-UUUUGU----UUUGCCAUUU----------UUCUUUGGCAACCACAACAAAGUGUUAGAGGGUCAGGUUAAUUGAUACACAGAC
..(((..((..((.(((((((....(((...((((-((((((----.((((((...----------.....))))))..)))).))))))..)))))))))).))....))....))).. ( -25.80)
>DroSec_CAF1 88503 100 + 1
UACUGCUUUUGAAGCUGGCUCAU---------UUUUUUUUGU-UUGUUUGCCAUUU----------UUCUUUGGCAACCACAACAAAGUGUUAGAAGGGCAGGUUAAUUGAUACACAGAC
..(((...(..(((((.((((.(---------(((.((((((-(((.((((((...----------.....)))))).)).)))))))....)))))))).))))..)..)....))).. ( -24.10)
>DroSim_CAF1 94804 109 + 1
UACUGCUUUUAAAGCUGGCCCCUUUUCUUUUUUUUUUUUUGU-UUGUUUGCCAUUU----------UUCUUUGGCAACCACAACAAAGUGUUAGAGGGGCAGGUUAAUUGAUACACAGAC
..(((...((((((((.((((((((...........((((((-(((.((((((...----------.....)))))).)).)))))))....)))))))).))))..))))....))).. ( -30.96)
>DroEre_CAF1 73468 103 + 1
UACUGCUUUUGAAGCUGGCCCCUGUUCUUUUUAUUU-------UUGUUCCCAAUUU----------UUCUUUGGCAACCACAACAAAGUGUUAGAGGGGCAGGUUAAUUGGUACACAGAC
...((((..(..((((.((((((.............-------..(((.((((...----------....)))).)))(((......)))....)))))).)))).)..))))....... ( -23.50)
>DroYak_CAF1 86828 101 + 1
UACUGCUUUUGAAGCUGACCCCUGCUCUGUUUUUUU-------UUUUGC--CAUUU----------UUCUUUGGCAACCACAACAAAGUGUUAGAGGGGCAGGUUAAUUGAUACACAGAC
..(((..((..((.(((.((((((((.((((.....-------..((((--((...----------.....))))))....)))).))).....)))))))).))....))....))).. ( -24.10)
>DroAna_CAF1 44755 120 + 1
UAUUGCUUUCAGUUUUUUUCCCUUUUUUUUCUUUCUGUGAUUUUUUUUACCCGUUUUUGUGUUUUAUUUUCUGGCAACCACAACAAAGUGUUAGAGGGACAGGUUAAUUGAUACGCAGAC
..((((..((((((..(((((((((.....((((.((((........(((........)))...........(....)))))..))))....)))))))..))..))))))...)))).. ( -20.70)
>consensus
UACUGCUUUUGAAGCUGGCCCCUGUUCUUUUUUUUUUUUUGU_UUGUUUGCCAUUU__________UUCUUUGGCAACCACAACAAAGUGUUAGAGGGGCAGGUUAAUUGAUACACAGAC
..(((...((((((((.((((((.................................................(....)(((......)))....)))))).))))..))))....))).. (-13.52 = -13.17 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:59 2006