Locus 2789

Sequence ID 2R_DroMel_CAF1
Location 9,730,628 – 9,730,755
Length 127
Max. P 0.981116
window4616 window4617 window4618 window4619

overview

Window 6

Location 9,730,628 – 9,730,726
Length 98
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 77.33
Mean single sequence MFE -20.80
Consensus MFE -12.56
Energy contribution -12.56
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.60
SVM decision value 0.58
SVM RNA-class probability 0.789801
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9730628 98 + 20766785
------AUAUCAGUCGC--UUUUCGCUGCUG---GCACGCUGGUCAUCUCACAGUAUAAUCCUGUGAUUUGGAUUGCAAAACGAAACAAAACACAAAAAUAUACUGCGA
------...(((((.((--.....)).))))---).............((.(((((((....((((.((((..(((.....)))..)))).))))....))))))).)) ( -22.70)
>DroVir_CAF1 342 98 + 1
-GUCUAAAAU----GGA--UUUUUGUUGUUG---CUACAGCCGAUAACUCACAGUAUAAUCCUGUGAUUUGAUUUUCAA-AAUAAACAAAACACAAAAGUAUACUGCGA
-((((.....----)))--)....(((((((---(....).)))))))((.(((((((....((((.((((.(((....-...))))))).))))....))))))).)) ( -19.70)
>DroPse_CAF1 362 93 + 1
------CGUU----CAC--ACUCUCUUGAUA---GCACGCCCAGCAUCUCACAGUAUAAUCCUGUGAUUUGCGUUUCAG-ACACAACAAAACACAAAAAUAUACUGCGA
------....----...--............---...(((...(((..((((((.......))))))..)))(((....-....)))..................))). ( -15.20)
>DroSec_CAF1 341 98 + 1
------AUAUCAUUCGC--UUUUUGCUGCUG---GCACGCUGGUCAUCUCACAGUAUAAUCCUGUGAUUUGAGUUGCAAAACGAAACAAAACACAAAAAUAUACUGCGA
------.......((((--....(((.....---))).((.(.(((..((((((.......))))))..))).).))............................)))) ( -20.20)
>DroEre_CAF1 334 101 + 1
------UGGUCAGUCAC--UUUCUGCUGCUGGCGGCACGCUGGUCAUCUCACAGUAUAAUCCUGUGAUUUGAUUUGCAAAACGAAACAAAACACAAAAAUAUACUGCGA
------((..((((...--....(((((....))))).))))..))..((.(((((((....((((.((((.((((.....)))).)))).))))....))))))).)) ( -28.10)
>DroAna_CAF1 349 101 + 1
U---U-UAAUUAUGCACUGUUUCAGCUGCUG---ACACGCUUGGCAUCUCACAGUAUAAUCCUGUGAUUUGAGUUUCAA-ACCAAACAAAACACAAAAAUAUACUGCGA
.---.-.....((((..(((.((((...)))---).)))....)))).((.(((((((....((((.(((..((((...-...)))).)))))))....))))))).)) ( -18.90)
>consensus
______AAAUCA_UCAC__UUUCUGCUGCUG___GCACGCUGGUCAUCUCACAGUAUAAUCCUGUGAUUUGAGUUGCAA_ACGAAACAAAACACAAAAAUAUACUGCGA
................................................((.(((((((....((((.((((...............)))).))))....))))))).)) (-12.56 = -12.56 +  -0.00)

alignment

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secondary structure

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Window 7

Location 9,730,628 – 9,730,726
Length 98
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 77.33
Mean single sequence MFE -27.92
Consensus MFE -21.71
Energy contribution -21.71
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.53
Structure conservation index 0.78
SVM decision value 1.88
SVM RNA-class probability 0.981116
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9730628 98 - 20766785
UCGCAGUAUAUUUUUGUGUUUUGUUUCGUUUUGCAAUCCAAAUCACAGGAUUAUACUGUGAGAUGACCAGCGUGC---CAGCAGCGAAAA--GCGACUGAUAU------
((((((((((.(((((((.((((..(.(.....).)..)))).))))))).))))))))))..............---(((..((.....--))..)))....------ ( -28.90)
>DroVir_CAF1 342 98 - 1
UCGCAGUAUACUUUUGUGUUUUGUUUAUU-UUGAAAAUCAAAUCACAGGAUUAUACUGUGAGUUAUCGGCUGUAG---CAACAACAAAAA--UCC----AUUUUAGAC-
((((((((((.(((((((.(((((((...-....))).)))).))))))).))))))))))(((....((....)---)...))).....--...----.........- ( -23.70)
>DroPse_CAF1 362 93 - 1
UCGCAGUAUAUUUUUGUGUUUUGUUGUGU-CUGAAACGCAAAUCACAGGAUUAUACUGUGAGAUGCUGGGCGUGC---UAUCAAGAGAGU--GUG----AACG------
((((((((((.(((((((.....((((((-.....))))))..))))))).))))))))))......(..((..(---(........)).--.))----..).------ ( -31.00)
>DroSec_CAF1 341 98 - 1
UCGCAGUAUAUUUUUGUGUUUUGUUUCGUUUUGCAACUCAAAUCACAGGAUUAUACUGUGAGAUGACCAGCGUGC---CAGCAGCAAAAA--GCGAAUGAUAU------
((((((((((.(((((((.((((....(((....))).)))).))))))).))))))))))........((.(((---.....)))....--)).........------ ( -26.60)
>DroEre_CAF1 334 101 - 1
UCGCAGUAUAUUUUUGUGUUUUGUUUCGUUUUGCAAAUCAAAUCACAGGAUUAUACUGUGAGAUGACCAGCGUGCCGCCAGCAGCAGAAA--GUGACUGACCA------
((((((((((.(((((((.((((.((.(.....).)).)))).))))))).))))))))))........((.(((.....))))).....--...........------ ( -27.10)
>DroAna_CAF1 349 101 - 1
UCGCAGUAUAUUUUUGUGUUUUGUUUGGU-UUGAAACUCAAAUCACAGGAUUAUACUGUGAGAUGCCAAGCGUGU---CAGCAGCUGAAACAGUGCAUAAUUA-A---A
((((((((((.(((((((.((((...(..-......).)))).))))))).))))))))))(((((.....))))---).(((.(((...)))))).......-.---. ( -30.20)
>consensus
UCGCAGUAUAUUUUUGUGUUUUGUUUCGU_UUGAAACUCAAAUCACAGGAUUAUACUGUGAGAUGACCAGCGUGC___CAGCAGCAAAAA__GCGA_UGAUAU______
((((((((((.(((((((.((((...............)))).))))))).))))))))))................................................ (-21.71 = -21.71 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,730,649 – 9,730,755
Length 106
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 81.31
Mean single sequence MFE -28.08
Consensus MFE -19.46
Energy contribution -20.96
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.83
Structure conservation index 0.69
SVM decision value 1.18
SVM RNA-class probability 0.927043
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9730649 106 + 20766785
UG---GCACGCUGGUCAUCUCACAGUAUAAUCCUGUGAUUUGGAUUGCAAAACGAAACAAAACACAAAAAUAUACUGCGAGGCGUCGAGACGUGUUAUUAACCCCGCCA
((---(((((((.(.(..(((.(((((((....((((.((((..(((.....)))..)))).))))....))))))).)))..).).)).)))))))............ ( -33.40)
>DroPse_CAF1 379 97 + 1
UA---GCACGCCCAGCAUCUCACAGUAUAAUCCUGUGAUUUGCGUUUCAG-ACACAACAAAACACAAAAAUAUACUGCGAGGCGUCAAGACGCC-GCUUCUU-------
.(---((.(((...(((..((((((.......))))))..)))(((....-....)))..................))).(((((....)))))-)))....------- ( -26.70)
>DroEre_CAF1 355 106 + 1
UGGCGGCACGCUGGUCAUCUCACAGUAUAAUCCUGUGAUUUGAUUUGCAAAACGAAACAAAACACAAAAAUAUACUGCGAGGCGUCGAGACGUGUGAUUCCCCCCA---
.((.((((((((.(.(..(((.(((((((....((((.((((.((((.....)))).)))).))))....))))))).)))..).).)).))))......)).)).--- ( -32.60)
>DroYak_CAF1 364 103 + 1
UG---GCACGCUGGUCAUCUCACAGUAUAAUCCUGUGAUUUGAGUUGCAAAAGGAAACAAAACACAAAAAUAUACUGCGAGGCGUCGAGACGUGUGAUUCCCCCCA---
..---(((((((.(.(..(((.(((((((....((((.((((.....)))).(....)....))))....))))))).)))..).).)).)))))...........--- ( -30.40)
>DroAna_CAF1 374 90 + 1
UG---ACACGCUUGGCAUCUCACAGUAUAAUCCUGUGAUUUGAGUUUCAA-ACCAAACAAAACACAAAAAUAUACUGCGAGGCGACGAGACAUG---------------
..---....(((((.(..(((.(((((((....((((.(((..((((...-...)))).)))))))....))))))).)))..).)))).)...--------------- ( -21.40)
>DroPer_CAF1 378 97 + 1
UA---GCACGCCCAGCAUCUCACAGUAUAAUCCUGUGAUUUGCGUUUCAG-ACACAACAAAACACAAAAAUAUACUGCGAGGCGUCAAGACGCC-GAUUCUU-------
..---...(((...(((..((((((.......))))))..)))(((....-....)))..................))).(((((....)))))-.......------- ( -24.00)
>consensus
UG___GCACGCUGGGCAUCUCACAGUAUAAUCCUGUGAUUUGAGUUGCAA_ACGAAACAAAACACAAAAAUAUACUGCGAGGCGUCGAGACGUG_GAUUCCC_______
......((((((.(.(..(((.(((((((....((((.((((...............)))).))))....))))))).)))..).).)).))))............... (-19.46 = -20.96 +   1.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,730,649 – 9,730,755
Length 106
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 81.31
Mean single sequence MFE -35.95
Consensus MFE -30.23
Energy contribution -29.76
Covariance contribution -0.47
Combinations/Pair 1.13
Mean z-score -3.70
Structure conservation index 0.84
SVM decision value 1.66
SVM RNA-class probability 0.970707
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9730649 106 - 20766785
UGGCGGGGUUAAUAACACGUCUCGACGCCUCGCAGUAUAUUUUUGUGUUUUGUUUCGUUUUGCAAUCCAAAUCACAGGAUUAUACUGUGAGAUGACCAGCGUGC---CA
.((((.(((((......(((....))).(((((((((((.(((((((.((((..(.(.....).)..)))).))))))).))))))))))).)))))....)))---). ( -37.90)
>DroPse_CAF1 379 97 - 1
-------AAGAAGC-GGCGUCUUGACGCCUCGCAGUAUAUUUUUGUGUUUUGUUGUGU-CUGAAACGCAAAUCACAGGAUUAUACUGUGAGAUGCUGGGCGUGC---UA
-------....(((-(.(((((.(.((.(((((((((((.(((((((.....((((((-.....))))))..))))))).))))))))))).))).))))))))---). ( -40.60)
>DroEre_CAF1 355 106 - 1
---UGGGGGGAAUCACACGUCUCGACGCCUCGCAGUAUAUUUUUGUGUUUUGUUUCGUUUUGCAAAUCAAAUCACAGGAUUAUACUGUGAGAUGACCAGCGUGCCGCCA
---..((.((.....((((.((.(.((.(((((((((((.(((((((.((((.((.(.....).)).)))).))))))).))))))))))).)).).)))))))).)). ( -37.20)
>DroYak_CAF1 364 103 - 1
---UGGGGGGAAUCACACGUCUCGACGCCUCGCAGUAUAUUUUUGUGUUUUGUUUCCUUUUGCAACUCAAAUCACAGGAUUAUACUGUGAGAUGACCAGCGUGC---CA
---..((((((........)))).(((((((((((((((.(((((((.((((...............)))).))))))).))))))))))).......)))).)---). ( -31.87)
>DroAna_CAF1 374 90 - 1
---------------CAUGUCUCGUCGCCUCGCAGUAUAUUUUUGUGUUUUGUUUGGU-UUGAAACUCAAAUCACAGGAUUAUACUGUGAGAUGCCAAGCGUGU---CA
---------------((((.((.(.((.(((((((((((.(((((((.((((...(..-......).)))).))))))).))))))))))).)).).)))))).---.. ( -30.50)
>DroPer_CAF1 378 97 - 1
-------AAGAAUC-GGCGUCUUGACGCCUCGCAGUAUAUUUUUGUGUUUUGUUGUGU-CUGAAACGCAAAUCACAGGAUUAUACUGUGAGAUGCUGGGCGUGC---UA
-------.......-.((((((.(.((.(((((((((((.(((((((.....((((((-.....))))))..))))))).))))))))))).))).))))))..---.. ( -37.60)
>consensus
_______GAGAAUC_CACGUCUCGACGCCUCGCAGUAUAUUUUUGUGUUUUGUUUCGU_UUGAAACUCAAAUCACAGGAUUAUACUGUGAGAUGACCAGCGUGC___CA
...............((((.((.(.((.(((((((((((.(((((((.((((...............)))).))))))).))))))))))).)).).))))))...... (-30.23 = -29.76 +  -0.47)

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 10:39:33 2006