Locus 7178

Sequence ID 3R_DroMel_CAF1
Location 18,922,933 – 18,923,081
Length 148
Max. P 0.831144
window11607 window11608 window11609

overview

Window 7

Location 18,922,933 – 18,923,041
Length 108
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 72.70
Mean single sequence MFE -23.57
Consensus MFE -9.43
Energy contribution -10.80
Covariance contribution 1.37
Combinations/Pair 1.35
Mean z-score -1.82
Structure conservation index 0.40
SVM decision value -0.04
SVM RNA-class probability 0.511712
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18922933 108 - 27905053
UGCUAUCUAUG-AUGAUACAGCAAAAUGUAGAUACAUCCAUUAUCUACUUGCUGUCGCAAGGAUAGCAA-GU-UGUAUUCUUCAGAUCUUAAGUUGAUUAAGGUAU--UCGUU-----
.........((-(.((((((((.....(((((((.......)))))))((((((((.....))))))))-))-))))))..))).(((((((.....)))))))..--.....----- ( -30.50)
>DroSec_CAF1 34211 108 - 1
UGCUAUCUAUAAAUGAUAUAGCAAACUAUAGAUAUAUCCAUUAUCUACUUACUGUCGCAAGGAUAGCAA-CU-UGUAUUCUUCAAAUA-GAAUGUGAUUAAAGUAU--UCAUU-----
((((((((.....((((((((....)))((((((.......)))))).....)))))...)))))))).-.(-..((((((......)-)))))..).........--.....----- ( -20.50)
>DroSim_CAF1 34020 109 - 1
UGCUAUCUAUAAAUGAUAUAGCAAAAUAUAGAUACAUCCAUUAUCUGCUUGCUGUCGCAAGGAUAGCAAAAU-AGUAUUCUUCAGAUA-CAAGUUGAUUAAAGUAU--UCGUU-----
((((((((.....((..(((((((....((((((.......)))))).)))))))..)).))))))))....-.(((((.....))))-)................--.....----- ( -20.90)
>DroEre_CAF1 34266 112 - 1
UGCUAUCUAUA-AUGACGAAGCAAAAUGUAGAUACAUGCAUUAUAUACUUGCUGUCGCAGGGAUAGCUA-CU-UGUAUUUUUCAGAUA-CAAGUUCAUUAAAGUAU--UCGCUGAAAU
.(((((((...-.((.((((((((((((((......))))))......))))).))))).))))))).(-((-((((((.....))))-)))))............--.......... ( -29.10)
>DroYak_CAF1 35092 112 - 1
UGCUAUCUAUG-AUGAUAUAGCAAAAUAUAGAUACAUGCAUUAUCAACCUGCUGUCGCAAGGAUAGCAA-CU-UGUAGUUUUCAGAUA-CAGGUUUAUUAAAGUAU--UCGUUUAAAU
(((((((....-..))..))))).....(((((..((((.(((..((((((.(((((((((........-))-))).(....).))))-))))))...))).))))--..)))))... ( -23.30)
>DroAna_CAF1 35108 97 - 1
UUUUAUCAAUA-UUGACUCGGU-----------------UGUAUCUACCUGUUGUUAAAAGGAUAGCAA-UUGUGGAUUCUUUAGAUG-UGAGGCCAUAAAAACAUGUCCAUU-AAUG
...........-(((((..(((-----------------.......)))....)))))..(((((....-((((((.(((........-.))).)))))).....)))))...-.... ( -17.10)
>consensus
UGCUAUCUAUA_AUGAUAUAGCAAAAUAUAGAUACAUCCAUUAUCUACUUGCUGUCGCAAGGAUAGCAA_CU_UGUAUUCUUCAGAUA_CAAGUUGAUUAAAGUAU__UCGUU_____
((((((((.....((((..(((((....((((((.......)))))).)))))))))...)))))))).................................................. ( -9.43 = -10.80 +   1.37)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,922,965 – 18,923,081
Length 116
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 75.33
Mean single sequence MFE -25.62
Consensus MFE -9.67
Energy contribution -10.20
Covariance contribution 0.53
Combinations/Pair 1.41
Mean z-score -2.15
Structure conservation index 0.38
SVM decision value 0.20
SVM RNA-class probability 0.628913
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18922965 116 + 27905053
AAUACA-AC-UUGCUAUCCUUGCGACAGCAAGUAGAUAAUGGAUGUAUCUACAUUUUGCUGUAUCAU-CAUAGAUAGCAAGUUGGAAGACUGGGAAGCCCAUUAAAUCCAAAAUAAUCA
....((-((-((((((((..((..((((((((((((((.......)))))))...))))))).....-))..))))))))))))......((((...)))).................. ( -37.50)
>DroSec_CAF1 34242 117 + 1
AAUACA-AG-UUGCUAUCCUUGCGACAGUAAGUAGAUAAUGGAUAUAUCUAUAGUUUGCUAUAUCAUUUAUAGAUAGCAAGUUGGAAGACUCUGAAGCCCAUUAAAUCCAAAAUAAUCA
....((-(.-((((((((..(((....)))(((((((.(((((....))))).)))))))............)))))))).)))................................... ( -24.50)
>DroSim_CAF1 34051 118 + 1
AAUACU-AUUUUGCUAUCCUUGCGACAGCAAGCAGAUAAUGGAUGUAUCUAUAUUUUGCUAUAUCAUUUAUAGAUAGCAAGUUGAAAGACUCGGAAGCCCAUUAAAUCCAAAAUAAUCA
......-...((((((((..(((....)))((((((..(((((....)))))..))))))............))))))))(((....)))..(((...........))).......... ( -24.90)
>DroEre_CAF1 34302 116 + 1
AAUACA-AG-UAGCUAUCCCUGCGACAGCAAGUAUAUAAUGCAUGUAUCUACAUUUUGCUUCGUCAU-UAUAGAUAGCAAGUUGGUAGACUCGGAAGCCCAUUAAAGCCAAAAUAAUCA
..((((-.(-((..(((.(.(((....))).).)))...))).))))(((((..((((((..(((..-....)))))))))...)))))...((....))................... ( -21.60)
>DroYak_CAF1 35128 116 + 1
ACUACA-AG-UUGCUAUCCUUGCGACAGCAGGUUGAUAAUGCAUGUAUCUAUAUUUUGCUAUAUCAU-CAUAGAUAGCAGGCUGAAAGGCGCCGAAGCCCAUUAAAGCCAAAAUAAUCA
......-..-.((((((((((((....))))).(((((..(((.(((....)))..)))..))))).-....)))))))((((....(((......)))......)))).......... ( -31.30)
>DroAna_CAF1 35145 97 + 1
AAUCCACAA-UUGCUAUCCUUUUAACAACAGGUAGAUACA-----------------ACCGAGUCAA-UAUUGAUAAAAUAGUGGGAUAUUGGAAUACUUUGUAGAU---AAGUAACCA
..(((((.(-((..((((............(((.......-----------------))).......-....)))).))).)))))....(((..(((((.......---))))).))) ( -13.90)
>consensus
AAUACA_AG_UUGCUAUCCUUGCGACAGCAAGUAGAUAAUGGAUGUAUCUAUAUUUUGCUAUAUCAU_UAUAGAUAGCAAGUUGGAAGACUCGGAAGCCCAUUAAAUCCAAAAUAAUCA
..........((((((((..(((....)))((((((..................))))))............))))))))....................................... ( -9.67 = -10.20 +   0.53)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,922,965 – 18,923,081
Length 116
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 75.33
Mean single sequence MFE -27.62
Consensus MFE -12.37
Energy contribution -12.52
Covariance contribution 0.14
Combinations/Pair 1.35
Mean z-score -2.13
Structure conservation index 0.45
SVM decision value 0.72
SVM RNA-class probability 0.831144
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18922965 116 - 27905053
UGAUUAUUUUGGAUUUAAUGGGCUUCCCAGUCUUCCAACUUGCUAUCUAUG-AUGAUACAGCAAAAUGUAGAUACAUCCAUUAUCUACUUGCUGUCGCAAGGAUAGCAA-GU-UGUAUU
..........(((.....((((...))))....)))((((((((((((.((-.(((..((((((...(((((((.......)))))))))))))))))).)))))))))-))-)..... ( -40.20)
>DroSec_CAF1 34242 117 - 1
UGAUUAUUUUGGAUUUAAUGGGCUUCAGAGUCUUCCAACUUGCUAUCUAUAAAUGAUAUAGCAAACUAUAGAUAUAUCCAUUAUCUACUUACUGUCGCAAGGAUAGCAA-CU-UGUAUU
........(((((......(((((....)))))))))).(((((((((.....((((((((....)))((((((.......)))))).....)))))...)))))))))-..-...... ( -22.20)
>DroSim_CAF1 34051 118 - 1
UGAUUAUUUUGGAUUUAAUGGGCUUCCGAGUCUUUCAACUUGCUAUCUAUAAAUGAUAUAGCAAAAUAUAGAUACAUCCAUUAUCUGCUUGCUGUCGCAAGGAUAGCAAAAU-AGUAUU
..(((((((((....(((((((....(((((......))))).((((((((..((......))...))))))))..)))))))....(((((....))))).....))))))-)))... ( -26.20)
>DroEre_CAF1 34302 116 - 1
UGAUUAUUUUGGCUUUAAUGGGCUUCCGAGUCUACCAACUUGCUAUCUAUA-AUGACGAAGCAAAAUGUAGAUACAUGCAUUAUAUACUUGCUGUCGCAGGGAUAGCUA-CU-UGUAUU
.((((.....(((((....)))))....))))...(((...(((((((...-.((.((((((((((((((......))))))......))))).))))).)))))))..-.)-)).... ( -28.20)
>DroYak_CAF1 35128 116 - 1
UGAUUAUUUUGGCUUUAAUGGGCUUCGGCGCCUUUCAGCCUGCUAUCUAUG-AUGAUAUAGCAAAAUAUAGAUACAUGCAUUAUCAACCUGCUGUCGCAAGGAUAGCAA-CU-UGUAGU
..........((((..((.((((....)).))))..))))((((((((.((-(((((...(((.............))))))))))...(((....))).)))))))).-..-...... ( -30.12)
>DroAna_CAF1 35145 97 - 1
UGGUUACUU---AUCUACAAAGUAUUCCAAUAUCCCACUAUUUUAUCAAUA-UUGACUCGGU-----------------UGUAUCUACCUGUUGUUAAAAGGAUAGCAA-UUGUGGAUU
(((.(((((---.......)))))..))).....((((.((((((((....-(((((..(((-----------------.......)))....)))))...))))).))-).))))... ( -18.80)
>consensus
UGAUUAUUUUGGAUUUAAUGGGCUUCCGAGUCUUCCAACUUGCUAUCUAUA_AUGAUAUAGCAAAAUAUAGAUACAUCCAUUAUCUACUUGCUGUCGCAAGGAUAGCAA_CU_UGUAUU
...............((((((((......))).......((((((((.......)))..)))))..............)))))......(((((((.....)))))))........... (-12.37 = -12.52 +   0.14)

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 12:39:19 2006