Locus 2302

Sequence ID 3L_DroMel_CAF1
Location 6,475,276 – 6,475,399
Length 123
Max. P 0.844729
window3554 window3555 window3556

overview

Window 4

Location 6,475,276 – 6,475,376
Length 100
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 83.62
Mean single sequence MFE -22.66
Consensus MFE -17.74
Energy contribution -17.92
Covariance contribution 0.18
Combinations/Pair 1.20
Mean z-score -1.80
Structure conservation index 0.78
SVM decision value 0.29
SVM RNA-class probability 0.668531
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6475276 100 + 23771897
G-ACUCAGUGGCUCUC--UGUUUGUGUUUUAAA-AUUUUAAACGUUGCAAAUGUUUUGCAACAUUUCGACGGCUUUACCAGCUGUGUGCUACUAGUAUUCCACU
.-(((.((((((.(..--.(((((.........-....)))))(((((((.....)))))))......((((((.....))))))).)))))))))........ ( -25.32)
>DroSec_CAF1 9802 101 + 1
AAACUCAGUGGCUCUC--UGUUUGUGUUUUAAA-AUUUUAAACGUUGCAAAUGUUUUGAAACAUUUCGACGGCUUUACCAGCUGUGUGCUACUAGUAUUCCACG
..(((.((((((.(..--((...((((((((((-((................))))))))))))..))((((((.....))))))).)))))))))........ ( -24.19)
>DroSim_CAF1 9896 100 + 1
A-ACUCAGUGGCUCUC--UGUUUGUGUUUUAAA-AUUUUAAACGUUGCAAAUGUUUUGCAACAUUUCGGCGGCUUUACCAGCUGUGUGCUACUAGUAUUCCACG
.-(((.((((((.(..--.(((((.........-....)))))(((((((.....)))))))......((((((.....))))))).)))))))))........ ( -25.52)
>DroEre_CAF1 10144 100 + 1
A-ACUCGCUGGUUCUC--UGUUUGUAUUUUGAA-AUUUUAAACGUUGCAAAUGUUUUGCAACAUUUCGACGGCUUUACCAGCUGUAUGCUACUAGUAUUCCUCU
.-....((((((...(--((((.....(((((.-...))))).(((((((.....))))))).....)))))....))))))...((((.....))))...... ( -22.00)
>DroYak_CAF1 10126 103 + 1
A-UUUCAGUGGUUCUCAGUGUUUGUAUUUUGAAAAUUUUAAACGUUGCAAAUGUUUUGCAACAUUUCGACGGCUUUACCAGCUGUGUGCUACUAGUAUUUCCCU
.-....((((((.(.((((....(((.(((((.....)))))(((((.(((((((....))))))))))))....)))..)))).).))))))........... ( -22.20)
>DroAna_CAF1 8888 83 + 1
A-CU--------GCAC--UGUUUGUAUUUUAAA-UUUUUAAGCGUUGCAAGUGUUUUGCAACAUUU-GACGGCCCUACCAGCUGUCCA--------AUCCCACU
.-..--------(((.--((((((.........-....)))))).)))(((((((....)))))))-((((((.......))))))..--------........ ( -16.72)
>consensus
A_ACUCAGUGGCUCUC__UGUUUGUAUUUUAAA_AUUUUAAACGUUGCAAAUGUUUUGCAACAUUUCGACGGCUUUACCAGCUGUGUGCUACUAGUAUUCCACU
......((((((.......(((((..............)))))((((((((...))))))))......((((((.....))))))..))))))........... (-17.74 = -17.92 +   0.18)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,475,276 – 6,475,376
Length 100
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 83.62
Mean single sequence MFE -21.92
Consensus MFE -15.07
Energy contribution -16.57
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.02
Structure conservation index 0.69
SVM decision value 0.09
SVM RNA-class probability 0.579636
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6475276 100 - 23771897
AGUGGAAUACUAGUAGCACACAGCUGGUAAAGCCGUCGAAAUGUUGCAAAACAUUUGCAACGUUUAAAAU-UUUAAAACACAAACA--GAGAGCCACUGAGU-C
(((((..(((((((........))))))).........(((((((((((.....))))))))))).....-...............--.....)))))....-. ( -24.80)
>DroSec_CAF1 9802 101 - 1
CGUGGAAUACUAGUAGCACACAGCUGGUAAAGCCGUCGAAAUGUUUCAAAACAUUUGCAACGUUUAAAAU-UUUAAAACACAAACA--GAGAGCCACUGAGUUU
.((((..(((((((........)))))))....(((.((((((((....))))))).).)))........-...............--.....))))....... ( -18.30)
>DroSim_CAF1 9896 100 - 1
CGUGGAAUACUAGUAGCACACAGCUGGUAAAGCCGCCGAAAUGUUGCAAAACAUUUGCAACGUUUAAAAU-UUUAAAACACAAACA--GAGAGCCACUGAGU-U
.((((..(((((((........)))))))...))))..(((((((((((.....))))))))))).....-.............((--(.......)))...-. ( -25.00)
>DroEre_CAF1 10144 100 - 1
AGAGGAAUACUAGUAGCAUACAGCUGGUAAAGCCGUCGAAAUGUUGCAAAACAUUUGCAACGUUUAAAAU-UUCAAAAUACAAACA--GAGAACCAGCGAGU-U
...((..(((((((........)))))))...)).((((((((((((((.....)))))))))))....(-(((............--)))).....)))..-. ( -22.60)
>DroYak_CAF1 10126 103 - 1
AGGGAAAUACUAGUAGCACACAGCUGGUAAAGCCGUCGAAAUGUUGCAAAACAUUUGCAACGUUUAAAAUUUUCAAAAUACAAACACUGAGAACCACUGAAA-U
..((...(((((((........)))))))...)).((((((((((((((.....)))))))))))....((((((............))))))....)))..-. ( -22.50)
>DroAna_CAF1 8888 83 - 1
AGUGGGAU--------UGGACAGCUGGUAGGGCCGUC-AAAUGUUGCAAAACACUUGCAACGCUUAAAAA-UUUAAAAUACAAACA--GUGC--------AG-U
....(.((--------(((((.(((.....))).)))-....(((((((.....))))))).........-.............))--)).)--------..-. ( -18.30)
>consensus
AGUGGAAUACUAGUAGCACACAGCUGGUAAAGCCGUCGAAAUGUUGCAAAACAUUUGCAACGUUUAAAAU_UUUAAAACACAAACA__GAGAGCCACUGAGU_U
...((..(((((((........)))))))...))....(((((((((((.....)))))))))))....................................... (-15.07 = -16.57 +   1.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,475,309 – 6,475,399
Length 90
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 81.82
Mean single sequence MFE -20.10
Consensus MFE -9.72
Energy contribution -10.88
Covariance contribution 1.17
Combinations/Pair 1.00
Mean z-score -3.30
Structure conservation index 0.48
SVM decision value 0.76
SVM RNA-class probability 0.844729
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6475309 90 - 23771897
UACAACCUAUAUAUAUA----AAAAAAAGUGGAAUACUAGUAGCACACAGCU--GGUAAAGCCGUCGAAAUGUUGC---AAAACAUUUGCAACGUUUAA
.................----.......((((..(((((((........)))--))))...))).).(((((((((---((.....))))))))))).. ( -21.00)
>DroPse_CAF1 11877 81 - 1
GACAA-----AUAUA------A-AAAAAGUGGAAU------AGCACACAGCUGUGGCAAAGCCGUCAAAUUGUUGCAACAAAACAUUCGAAACGUUUUA
(((..-----.....------.-..........((------(((.....)))))(((...))))))....((((.......)))).............. ( -11.70)
>DroSec_CAF1 9836 89 - 1
UACAACCUAUAUA-----AAAAAAAAACGUGGAAUACUAGUAGCACACAGCU--GGUAAAGCCGUCGAAAUGUUUC---AAAACAUUUGCAACGUUUAA
.............-----......((((((((..(((((((........)))--))))...))((..(((((((..---..))))))))).)))))).. ( -17.70)
>DroSim_CAF1 9929 94 - 1
UACAACCUAUAUAUAAAAAAAAAAAAACGUGGAAUACUAGUAGCACACAGCU--GGUAAAGCCGCCGAAAUGUUGC---AAAACAUUUGCAACGUUUAA
............................((((..(((((((........)))--))))...))))..(((((((((---((.....))))))))))).. ( -24.00)
>DroEre_CAF1 10177 83 - 1
UACAACCCAUAA-----------AAAAAGAGGAAUACUAGUAGCAUACAGCU--GGUAAAGCCGUCGAAAUGUUGC---AAAACAUUUGCAACGUUUAA
............-----------.....((((..(((((((........)))--))))...)).)).(((((((((---((.....))))))))))).. ( -21.60)
>DroYak_CAF1 10162 88 - 1
UACAACAUAUAUAUA------AUAAAGAGGGAAAUACUAGUAGCACACAGCU--GGUAAAGCCGUCGAAAUGUUGC---AAAACAUUUGCAACGUUUAA
...............------.....((.((...(((((((........)))--))))...)).)).(((((((((---((.....))))))))))).. ( -24.60)
>consensus
UACAACCUAUAUAUA______AAAAAAAGUGGAAUACUAGUAGCACACAGCU__GGUAAAGCCGUCGAAAUGUUGC___AAAACAUUUGCAACGUUUAA
..............................((..((((...(((.....)))..))))...))....(((((((((............))))))))).. ( -9.72 = -10.88 +   1.17)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:03 2006