Locus 725

Sequence ID 2L_DroMel_CAF1
Location 2,097,969 – 2,098,101
Length 132
Max. P 0.999053
window1187 window1188 window1189 window1190

overview

Window 7

Location 2,097,969 – 2,098,066
Length 97
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.57
Mean single sequence MFE -31.85
Consensus MFE -13.76
Energy contribution -14.59
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -2.61
Structure conservation index 0.43
SVM decision value 0.08
SVM RNA-class probability 0.572320
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2097969 97 + 22407834
UAAUGCGCUCAAAGCGCAUUCAAAGCUGGCA----UUGAAUUAUUGAUU-------C--UCCCUUUU-G-GCCAGCCAC-----UGUCAUCAGCCGG---CUAGCCAAAAAGUGGCCAAC
.(((((((.....)))))))......((((.----..(((((...))))-------)--....((((-(-((.((((.(-----((....)))..))---)).)))))))....)))).. ( -34.20)
>DroSec_CAF1 115060 97 + 1
UAAUGCGCUCAAAGCGCAUUCAAAGCUGGCA----UUGAAUUAUCGAUG-------C--UCCCUUUU-G-GCCAGCCAC-----GGUCAUUAGCCGG---CUAGCCAAAAAGUGGCCAAC
.(((((((.....)))))))....(((((((----((((....))))))-------)--)...((((-(-((.((((..-----(((.....)))))---)).)))))))...))).... ( -37.00)
>DroEre_CAF1 117680 95 + 1
UAAUGCGCUCAAAGCGCAUUCAAAGCUG--A----AUGAAUUAUUGAUG-------C--UCCCUUUU-G-GUCAGCCAC-----GGUCAUUAGCCGG---CUAGCCAAAAAGUUGCCAAG
.(((((((.....)))))))........--.----.............(-------(--..(.((((-(-(..((((..-----(((.....)))))---))..)))))).)..)).... ( -27.70)
>DroYak_CAF1 119818 95 + 1
UAAUGCGCUCAAAGCGCAUACAAAGCUG--A----AUGAAUUAUUGAUG-------C--UCCCUUUUCG-GCCAGCCAC-----GGUCAUUAGCCGG---CUAGCCAA-AAGUGGCCAAC
..((((((.....))))))....((((.--(----(((...)))).).)-------)--)(((((((.(-((.((((..-----(((.....)))))---)).)))))-))).))..... ( -28.30)
>DroAna_CAF1 118791 101 + 1
UAAUGCGCUCAAAGCGCAUUCAAAGUUGCCAAAACUUGAAUUAUUGAUG-------GUGUCACUGCU-G-GAUAGCCAC-----GGUCAUUAGCCAA---CUAGCCAAAAAGUGACCA--
...(((((.....)))))(((((.(((.....)))))))).........-------(.((((((..(-(-(.(((....-----(((.....)))..---))).)))...))))))).-- ( -26.40)
>DroPer_CAF1 169797 112 + 1
UAAUGCGCUCAAAGCGCAUUCAAAGUUUCGA----UUGAAUUAUUAAUGGGUCGGGC--GCCCAUCUGGGGCUGGCCACGGCCGGGUCAUUAGCCAGAAUGUAGCCAAAAACUGGCCA--
.(((((((.....)))))))......(((..----..............((((((((--((((.....))))..))).))))).(((.....))).)))....((((.....))))..-- ( -37.50)
>consensus
UAAUGCGCUCAAAGCGCAUUCAAAGCUG_CA____UUGAAUUAUUGAUG_______C__UCCCUUUU_G_GCCAGCCAC_____GGUCAUUAGCCGG___CUAGCCAAAAAGUGGCCAAC
.(((((((.....)))))))......................................................(((((.....(((................))).....))))).... (-13.76 = -14.59 +   0.83)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,097,969 – 2,098,066
Length 97
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.57
Mean single sequence MFE -36.77
Consensus MFE -21.08
Energy contribution -20.88
Covariance contribution -0.19
Combinations/Pair 1.20
Mean z-score -3.26
Structure conservation index 0.57
SVM decision value 1.50
SVM RNA-class probability 0.959594
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2097969 97 - 22407834
GUUGGCCACUUUUUGGCUAG---CCGGCUGAUGACA-----GUGGCUGGC-C-AAAAGGGA--G-------AAUCAAUAAUUCAA----UGCCAGCUUUGAAUGCGCUUUGAGCGCAUUA
((((((..((((((((((((---(((.(((....))-----)))))))))-)-))))))..--(-------(((.....))))..----.))))))....(((((((.....))))))). ( -47.90)
>DroSec_CAF1 115060 97 - 1
GUUGGCCACUUUUUGGCUAG---CCGGCUAAUGACC-----GUGGCUGGC-C-AAAAGGGA--G-------CAUCGAUAAUUCAA----UGCCAGCUUUGAAUGCGCUUUGAGCGCAUUA
((((((..((((((((((((---(((((....).))-----..)))))))-)-))))))..--.-------....((....))..----.))))))....(((((((.....))))))). ( -43.60)
>DroEre_CAF1 117680 95 - 1
CUUGGCAACUUUUUGGCUAG---CCGGCUAAUGACC-----GUGGCUGAC-C-AAAAGGGA--G-------CAUCAAUAAUUCAU----U--CAGCUUUGAAUGCGCUUUGAGCGCAUUA
....((..((((((((.(((---(((((....).))-----..))))).)-)-))))))..--)-------).............----.--........(((((((.....))))))). ( -31.40)
>DroYak_CAF1 119818 95 - 1
GUUGGCCACUU-UUGGCUAG---CCGGCUAAUGACC-----GUGGCUGGC-CGAAAAGGGA--G-------CAUCAAUAAUUCAU----U--CAGCUUUGUAUGCGCUUUGAGCGCAUUA
(.((.((..((-((((((((---(((((....).))-----..)))))))-)))))..)).--.-------)).)..........----.--.........((((((.....)))))).. ( -32.30)
>DroAna_CAF1 118791 101 - 1
--UGGUCACUUUUUGGCUAG---UUGGCUAAUGACC-----GUGGCUAUC-C-AGCAGUGACAC-------CAUCAAUAAUUCAAGUUUUGGCAACUUUGAAUGCGCUUUGAGCGCAUUA
--..((((((..((((.(((---(((((....).))-----)..)))).)-)-)).))))))..-------........(((((((((.....))).))))))((((.....)))).... ( -27.50)
>DroPer_CAF1 169797 112 - 1
--UGGCCAGUUUUUGGCUACAUUCUGGCUAAUGACCCGGCCGUGGCCAGCCCCAGAUGGGC--GCCCGACCCAUUAAUAAUUCAA----UCGAAACUUUGAAUGCGCUUUGAGCGCAUUA
--.((((.(((.(((((((.....))))))).)))..))))(.(((..((((.....))))--))))............((((((----........))))))((((.....)))).... ( -37.90)
>consensus
GUUGGCCACUUUUUGGCUAG___CCGGCUAAUGACC_____GUGGCUGGC_C_AAAAGGGA__G_______CAUCAAUAAUUCAA____UG_CAGCUUUGAAUGCGCUUUGAGCGCAUUA
..((((((.....))))))....(((((((............)))))))...................................................(((((((.....))))))). (-21.08 = -20.88 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,098,005 – 2,098,101
Length 96
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 80.21
Mean single sequence MFE -27.00
Consensus MFE -16.34
Energy contribution -17.06
Covariance contribution 0.72
Combinations/Pair 1.14
Mean z-score -1.79
Structure conservation index 0.61
SVM decision value 0.17
SVM RNA-class probability 0.614968
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2098005 96 + 22407834
UUAUUGAUUCUCCCUUUU-GGCCAGCCACUGUCAUCAGCCGGCUAGCCAAAAAGUGGCCAACGAAACUCUGGAGGCGAAAUA-GCCCCCAA----AACUGAA
...(((.((..(((((((-(((.((((.(((....)))..)))).))).))))).))..))))).....(((.(((......-))).))).----....... ( -28.40)
>DroSec_CAF1 115096 96 + 1
UUAUCGAUGCUCCCUUUU-GGCCAGCCACGGUCAUUAGCCGGCUAGCCAAAAAGUGGCCAACGAAACUCUGGAGGCGAAAGA-GCCCCCAA----AACUGAA
...(((..((..(.((((-(((.((((..(((.....))))))).))))))).)..))...))).....(((.(((......-))).))).----....... ( -32.80)
>DroSim_CAF1 114964 96 + 1
UUAUUGAUGCUCCCUUUU-GGCCAGCCACGGUCAUUAGCCGGCUAGCCAAAAAGUGGCCAACGAAACUCUGGAGGCGAAAGA-GCCCCCAA----AACUGAA
...(((..((..(.((((-(((.((((..(((.....))))))).))))))).)..))...))).....(((.(((......-))).))).----....... ( -30.70)
>DroEre_CAF1 117714 79 + 1
UUAUUGAUGCUCCCUUUU-GGUCAGCCACGGUCAUUAGCCGGCUAGCCAAAAAGUUGCCAAGAC-----------------A-GCCUUUGA----AACUGGA
..........(((.((((-((..((((..(((.....)))))))..))))))((((..((((..-----------------.-...)))).----))))))) ( -20.40)
>DroYak_CAF1 119852 87 + 1
UUAUUGAUGCUCCCUUUUCGGCCAGCCACGGUCAUUAGCCGGCUAGCCAA-AAGUGGCCAACGAAGC--------------AGGCCUUCCAACUGAACUGAA
...(((.((..(((((((.(((.((((..(((.....))))))).)))))-))).)).)).)))..(--------------((..(........)..))).. ( -22.70)
>consensus
UUAUUGAUGCUCCCUUUU_GGCCAGCCACGGUCAUUAGCCGGCUAGCCAAAAAGUGGCCAACGAAACUCUGGAGGCGAAA_A_GCCCCCAA____AACUGAA
...(((.((.((.(((((.(((.((((..(((.....))))))).))).))))).)).)).)))...................................... (-16.34 = -17.06 +   0.72)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,098,005 – 2,098,101
Length 96
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 80.21
Mean single sequence MFE -38.02
Consensus MFE -21.78
Energy contribution -25.22
Covariance contribution 3.44
Combinations/Pair 1.03
Mean z-score -3.81
Structure conservation index 0.57
SVM decision value 3.35
SVM RNA-class probability 0.999053
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2098005 96 - 22407834
UUCAGUU----UUGGGGGC-UAUUUCGCCUCCAGAGUUUCGUUGGCCACUUUUUGGCUAGCCGGCUGAUGACAGUGGCUGGCC-AAAAGGGAGAAUCAAUAA
.....((----((((((((-......))))))))))....((((.(..(((((((((((((((.(((....))))))))))))-))))))..)...)))).. ( -44.40)
>DroSec_CAF1 115096 96 - 1
UUCAGUU----UUGGGGGC-UCUUUCGCCUCCAGAGUUUCGUUGGCCACUUUUUGGCUAGCCGGCUAAUGACCGUGGCUGGCC-AAAAGGGAGCAUCGAUAA
.....((----((((((((-......))))))))))..(((...((..(((((((((((((((((....).))..))))))))-))))))..))..)))... ( -45.80)
>DroSim_CAF1 114964 96 - 1
UUCAGUU----UUGGGGGC-UCUUUCGCCUCCAGAGUUUCGUUGGCCACUUUUUGGCUAGCCGGCUAAUGACCGUGGCUGGCC-AAAAGGGAGCAUCAAUAA
.....((----((((((((-......))))))))))....((((((..(((((((((((((((((....).))..))))))))-))))))..))..)))).. ( -43.30)
>DroEre_CAF1 117714 79 - 1
UCCAGUU----UCAAAGGC-U-----------------GUCUUGGCAACUUUUUGGCUAGCCGGCUAAUGACCGUGGCUGACC-AAAAGGGAGCAUCAAUAA
..(((((----.....)))-)-----------------).....((..((((((((.((((((((....).))..))))).))-))))))..))........ ( -24.50)
>DroYak_CAF1 119852 87 - 1
UUCAGUUCAGUUGGAAGGCCU--------------GCUUCGUUGGCCACUU-UUGGCUAGCCGGCUAAUGACCGUGGCUGGCCGAAAAGGGAGCAUCAAUAA
....((((........((((.--------------((...)).))))..((-(((((((((((((....).))..))))))))))))...))))........ ( -32.10)
>consensus
UUCAGUU____UUGGGGGC_U_UUUCGCCUCCAGAGUUUCGUUGGCCACUUUUUGGCUAGCCGGCUAAUGACCGUGGCUGGCC_AAAAGGGAGCAUCAAUAA
............(((((((.......))))))).......((((((..(((((((((((((((.(........)))))))))).))))))..))..)))).. (-21.78 = -25.22 +   3.44)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:59 2006