Locus 4783

Sequence ID	3L_DroMel_CAF1
Location	13,406,986 – 13,407,086
Length	100
Max. P	0.953656

overview

Window 3

Location	13,406,986 – 13,407,086
Length	100
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.87
Mean single sequence MFE	-33.45
Consensus MFE	-30.42
Energy contribution	-30.75
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.72
Structure conservation index	0.91
SVM decision value	0.91
SVM RNA-class probability	0.880314
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13406986 100 + 23771897
---UUUCAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGG-UGA-UAA--ACU-UUUUUUUU------------
---..(((.((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))).-)))-...--...-........------------ ( -34.20)
>DroVir_CAF1 5601 113 + 1
AGUUCCCAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAUG-AUA-C-A--AUUAUUUU-UUAAAUUUUCAAUG-
..........(((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))..-...-.-.--........-..............- ( -28.60)
>DroGri_CAF1 5402 114 + 1
UGCGUUCAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGA-UGA-UUU--ACU-UUUU-GCAAUUGCUUUUUUA
((((.(((.((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))).-)))-...--...-...)-)))............ ( -35.60)
>DroYak_CAF1 4099 105 + 1
---UUUCAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGG-UGAAGUA--CU----UUUUUGCAUCU-----UA
---(((((.((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))).-)))))..--..----...........-----.. ( -35.50)
>DroAna_CAF1 3842 112 + 1
--CUUUCAGCUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGGAUGA-UUA--AUU-UUUUUGUAUAUUU-UUU-UA
--...(((.((((((((((((((.......)))))).(((((.......)))))..((((..((......)).))))))))))))..)))-...--...-.............-...-.. ( -33.70)
>DroPer_CAF1 4314 104 + 1
---UUUCAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAUG---A-UUGGGAU----UUGAUUUAUCU-----CG
---..(((..(((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))))---)-..(((((----.......))))-----). ( -33.10)
>consensus
___UUUCAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGG_UGA_UUA__AUU_UUUUUUUAAAUCU_____UA
.........((((((((((((((.......)))))).(((((.......)))))..((((..((......)).))))))))))))................................... (-30.42 = -30.75 +   0.33)

alignment

secondary structure

dotplot

Window 4

Location	13,406,986 – 13,407,086
Length	100
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.87
Mean single sequence MFE	-34.22
Consensus MFE	-30.53
Energy contribution	-30.87
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.28
Structure conservation index	0.89
SVM decision value	1.43
SVM RNA-class probability	0.953656
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13406986 100 - 23771897
------------AAAAAAAA-AGU--UUA-UCA-CCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUGAAA---
------------........-...--...-(((-.((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).))))))))).)))..--- ( -35.20)
>DroVir_CAF1 5601 113 - 1
-CAUUGAAAAUUUAA-AAAAUAAU--U-G-UAU-CAUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUGGGAACU
-..............-.......(--(-.-((.-..(((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).))))))))..)).))... ( -30.50)
>DroGri_CAF1 5402 114 - 1
UAAAAAAGCAAUUGC-AAAA-AGU--AAA-UCA-UCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUGAACGCA
.......((..((((-....-.))--)).-(((-.((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).))))))))).)))..)). ( -38.90)
>DroYak_CAF1 4099 105 - 1
UA-----AGAUGCAAAAA----AG--UACUUCA-CCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUGAAA---
..-----...........----..--...((((-.((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).))))))))).)))).--- ( -35.90)
>DroAna_CAF1 3842 112 - 1
UA-AAA-AAAUAUACAAAAA-AAU--UAA-UCAUCCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGCUGAAAG--
..-...-.............-...--...-(((..((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).))))))))).)))...-- ( -33.60)
>DroPer_CAF1 4314 104 - 1
CG-----AGAUAAAUCAA----AUCCCAA-U---CAUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUGAAA---
.(-----(......))..----....(((-(---..(((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).))))))))))))...--- ( -31.20)
>consensus
UA_____AAAUAUAAAAAAA_AAU__UAA_UCA_CCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUGAAA___
...................................((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).)))))))))......... (-30.53 = -30.87 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:12 2006