Locus 2762

Sequence ID	2L_DroMel_CAF1
Location	7,788,370 – 7,788,493
Length	123
Max. P	0.998021

overview

Window 9

Location	7,788,370 – 7,788,477
Length	107
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	75.11
Mean single sequence MFE	-29.13
Consensus MFE	-13.80
Energy contribution	-13.05
Covariance contribution	-0.75
Combinations/Pair	1.33
Mean z-score	-2.55
Structure conservation index	0.47
SVM decision value	1.89
SVM RNA-class probability	0.981482
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7788370 107 + 22407834
AAUAUUGUUGAAAGCUUUUAUAGA----AUACCUUCACACAGUAGUUCCAAAAAGGGUGCAUCACAUAGACGCUGAGGAAGCUCGUGUCUAUACUGCUGUACUACGG--AAUA
..((((((((((.(..(((...))----)..).)))).))))))(((((......((((((.((.((((((((.(((....)))))))))))..)).))))))..))--))). ( -30.00)
>DroPse_CAF1 1287 107 + 1
----UUCUUUGGUGUGAAAAUAGAUCACUUACCUUAACACAAUAGUUCCAGAAUGGGUGCAUUAUAUAGACACUGACGAAACCAGUGUCUAUGCAGUUGUACUAUGG--GAAA
----......(((((((.......))))..)))............(((((.....((((((...(((((((((((.......)))))))))))....)))))).)))--)).. ( -30.70)
>DroSec_CAF1 1273 107 + 1
UAUAUUCUUGGAAGCUUUUAUAGA----AUACCUUCACACAGUAGUUCCAAAAAGGGUGCAUCACAUAGACGCUGAGGAAGCUCGUGUCUAUACUGCUGUACUACGG--AAUA
..(((((((((...........((----(....)))..(((((((((((.....)))........((((((((.(((....))))))))))))))))))).))).))--)))) ( -29.20)
>DroSim_CAF1 1268 107 + 1
UAUAUUCUUGGAAGCUUUUAUAGA----AUACCUUCACACAGUAGUUCCAAAAAGGGUGCAUCACAUAGACGCUGAGGAAGCUCGUGUCUAUACUGCUGUACUACGG--AAUA
..(((((((((...........((----(....)))..(((((((((((.....)))........((((((((.(((....))))))))))))))))))).))).))--)))) ( -29.20)
>DroWil_CAF1 91794 109 + 1
UAUGACCUAGUUAUUGCUAUUAGU----UUACCUUGACGCAGGCAUUCCAAAAUGGAUGCAUUACAUAGACACUAAGAAAACUCGUGUCUAUGCUGUUAUACUGUAAAGAAGA
.......((((....))))....(----((((......((((((((((......))))))....(((((((((...........)))))))))))))......)))))..... ( -25.00)
>DroPer_CAF1 2034 107 + 1
----UUCUUUGGUGUGAAAAUAGAUCACUUACCUUAACACAAUAGUUCCAGAAUGGGUGCAUUAUAUAGACACUGACGAAACCAGUGUCUAUGCAGUUGUACUAUGG--GAAA
----......(((((((.......))))..)))............(((((.....((((((...(((((((((((.......)))))))))))....)))))).)))--)).. ( -30.70)
>consensus
UAUAUUCUUGGAAGCGUUAAUAGA____AUACCUUCACACAGUAGUUCCAAAAAGGGUGCAUCACAUAGACACUGAGGAAACUCGUGUCUAUACUGCUGUACUACGG__AAUA
......................................(((((.(((((.....)))........((((((((...........)))))))))).)))))............. (-13.80 = -13.05 +  -0.75)

alignment

secondary structure

dotplot

Window 0

Location	7,788,399 – 7,788,493
Length	94
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	70.00
Mean single sequence MFE	-24.52
Consensus MFE	-13.05
Energy contribution	-13.00
Covariance contribution	-0.05
Combinations/Pair	1.42
Mean z-score	-2.84
Structure conservation index	0.53
SVM decision value	2.99
SVM RNA-class probability	0.998021
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7788399 94 + 22407834
UUCACACAGUAGUUCCAAAAAGGGUGCAUCACAUAGACGCUGAGGAAGCUCGUGUCUAUACUGCUGUACUACGG--AAUAAA--UAAUAAGA---UAUUGA
......((((((((((......((((((.((.((((((((.(((....)))))))))))..)).))))))..))--)))...--........---))))). ( -25.70)
>DroVir_CAF1 83812 98 + 1
UUCACGCAGGAAUUCCAGAACGGAUGCAUUAUAUAGACACUCAGAAAACUAGUGUCUAUGCUGUUGUACUGUCA--ACGAAACAUAAUA-AAUAAUGAAAA
((((....((....)).((.(((.((((.((((((((((((.((....)))))))))))).)).))))))))).--.............-.....)))).. ( -21.80)
>DroWil_CAF1 91823 97 + 1
UUGACGCAGGCAUUCCAAAAUGGAUGCAUUACAUAGACACUAAGAAAACUCGUGUCUAUGCUGUUAUACUGUAAAGAAGAAC--AAAUA-AAUA-UGUAGG
.....((((((((((......))))))....(((((((((...........)))))))))........))))..........--.....-....-...... ( -22.10)
>DroMoj_CAF1 76743 97 + 1
UUUACGCAAGCAUUCCAGAAGGGAUGCAUAACAUAGACGCUCAGAAGGCUGGUAUCUAUGCUAUUGUACUGGAU--GAGAAAGAUAACA-GACA-UGUUAA
.....(((((((((((....)))))))....((((((..(.(((....))))..))))))...)))).......--........(((((-....-))))). ( -25.70)
>DroAna_CAF1 1280 91 + 1
UUUACGCAGUAAUUCCAGAAGGGGUGCAUAACAUAGACACUUAGCCAACUAGUGUCUAUGCUAUUGUACUGGAA--AAAA-----AACCACA---UACUCU
.....(.((((...((....))((((((((.((((((((((.((....)))))))))))).)).))))))((..--....-----..))...---))))). ( -23.10)
>DroPer_CAF1 2063 96 + 1
UUAACACAAUAGUUCCAGAAUGGGUGCAUUAUAUAGACACUGACGAAACCAGUGUCUAUGCAGUUGUACUAUGG--GAAAAAGAUAGUGAAA---UUUUCA
....(((.((..(((((.....((((((...(((((((((((.......)))))))))))....)))))).)))--)).....)).)))...---...... ( -28.70)
>consensus
UUCACGCAGGAAUUCCAGAAGGGAUGCAUUACAUAGACACUCAGAAAACUAGUGUCUAUGCUGUUGUACUGUAA__AAGAAA__UAAUA_AA___UGUUAA
.....((((....(((.....))).......(((((((((.(((....))))))))))))...)))).................................. (-13.05 = -13.00 +  -0.05)

alignment

secondary structure

dotplot

Window 1

Location	7,788,399 – 7,788,493
Length	94
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	70.00
Mean single sequence MFE	-23.79
Consensus MFE	-12.59
Energy contribution	-12.53
Covariance contribution	-0.05
Combinations/Pair	1.40
Mean z-score	-2.67
Structure conservation index	0.53
SVM decision value	2.80
SVM RNA-class probability	0.997086
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7788399 94 - 22407834
UCAAUA---UCUUAUUA--UUUAUU--CCGUAGUACAGCAGUAUAGACACGAGCUUCCUCAGCGUCUAUGUGAUGCACCCUUUUUGGAACUACUGUGUGAA
......---........--(((((.--(.(((((...(((.(((((((.((((....))).).)))))))...)))..((.....)).))))).).))))) ( -20.80)
>DroVir_CAF1 83812 98 - 1
UUUUCAUUAUU-UAUUAUGUUUCGU--UGACAGUACAACAGCAUAGACACUAGUUUUCUGAGUGUCUAUAUAAUGCAUCCGUUCUGGAAUUCCUGCGUGAA
....((((((.-...........((--((......))))...(((((((((((....)).)))))))))))))))..(((((...((....)).))).)). ( -21.80)
>DroWil_CAF1 91823 97 - 1
CCUACA-UAUU-UAUUU--GUUCUUCUUUACAGUAUAACAGCAUAGACACGAGUUUUCUUAGUGUCUAUGUAAUGCAUCCAUUUUGGAAUGCCUGCGUCAA
......-....-.....--...........(((.......(((((((((((((....))).))))))))))...((((((.....)).)))))))...... ( -22.30)
>DroMoj_CAF1 76743 97 - 1
UUAACA-UGUC-UGUUAUCUUUCUC--AUCCAGUACAAUAGCAUAGAUACCAGCCUUCUGAGCGUCUAUGUUAUGCAUCCCUUCUGGAAUGCUUGCGUAAA
.(((((-....-)))))........--......(((.((((((((((..((((....))).)..))))))))))((((.((....)).))))....))).. ( -23.40)
>DroAna_CAF1 1280 91 - 1
AGAGUA---UGUGGUU-----UUUU--UUCCAGUACAAUAGCAUAGACACUAGUUGGCUAAGUGUCUAUGUUAUGCACCCCUUCUGGAAUUACUGCGUAAA
....((---((..((.-----....--((((((....((((((((((((((((....)).)))))))))))))).........))))))..))..)))).. ( -33.42)
>DroPer_CAF1 2063 96 - 1
UGAAAA---UUUCACUAUCUUUUUC--CCAUAGUACAACUGCAUAGACACUGGUUUCGUCAGUGUCUAUAUAAUGCACCCAUUCUGGAACUAUUGUGUUAA
.(((((---...........)))))--.(((((((....((((((((((((((.....)))))))))).....)))).((.....))...))))))).... ( -21.00)
>consensus
UCAACA___UU_UAUUA__UUUCUU__UUACAGUACAACAGCAUAGACACUAGUUUUCUCAGUGUCUAUGUAAUGCACCCAUUCUGGAAUUACUGCGUAAA
........................................(((((((((((((....))).)))))))))).(((((.((.....))......)))))... (-12.59 = -12.53 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:37 2006