Locus 6

Sequence ID 4_DroMel_CAF1
Location 90,786 – 91,015
Length 229
Max. P 0.924328
window8 window9 window10 window11

overview

Window 8

Location 90,786 – 90,898
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.51
Mean single sequence MFE -31.05
Consensus MFE -19.31
Energy contribution -20.25
Covariance contribution 0.94
Combinations/Pair 1.11
Mean z-score -2.13
Structure conservation index 0.62
SVM decision value 0.29
SVM RNA-class probability 0.669389
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 90786 112 + 1281640
GAUACUCAUCAGAUAGAU----AUAUGUAUA----CGUGUAACUAUGCAUGUAUAUGUAAACACGGCAUUGGAUCCUCUGCUUCGAAUGCAGAGAGCCGACAGUACUCACACACACCCUG
((((((............----.((((((((----((((((....))))))))))))))....((((........((((((.......)))))).))))..)))).))............ ( -29.20)
>DroSec_CAF1 36515 112 + 1
GAUACUCAUAAGAUAGAU----AUAUGUAUA----CGUAUAACUAUGCAUGUAUAUGUAAACACGGGAUCGGAUCCUAUGCUUCGAAUGCAGAGAGCCGACAGUACUCACACACACCCUU
.................(----(((((((((----.((((....)))).)))))))))).....(((.((((.((...(((.......)))..)).))))..((......))...))).. ( -23.40)
>DroEre_CAF1 51151 120 + 1
GAUACCCAUGAGCUAUACAUGCAUAUGUACACGUACGUACUCCUAUGCAUGUAUAUGUAAACACGGGAUCGGAUCCUCUGCUUCGAAUGCAGAGAGCCGACAUUACUCACACACACCCUG
....(((.((.((((((((((((((.((((......))))...)))))))))))).))...)).))).((((...((((((.......))))))..)))).................... ( -40.20)
>DroYak_CAF1 58938 114 + 1
GACAUUCAUGAGAUAUA------UAUGUACACACGCGUACACCGCUGCAUGUAUAUGUAAACACGGGAUCGGAUCCUCUGCUUCGAGUGCAGAGAGCCGACAGUACUCACACACACCCUG
........((((...((------((((((((((.(((.....)))))..))))))))))...((..(.((((...((((((.......))))))..))))).)).))))........... ( -31.40)
>consensus
GAUACUCAUGAGAUAGAU____AUAUGUACA____CGUACAACUAUGCAUGUAUAUGUAAACACGGGAUCGGAUCCUCUGCUUCGAAUGCAGAGAGCCGACAGUACUCACACACACCCUG
......................(((((((((....((((....))))..)))))))))......(((.((((...((((((.......))))))..))))..((......))...))).. (-19.31 = -20.25 +   0.94)

alignment

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secondary structure

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dotplot

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Window 9

Location 90,786 – 90,898
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.51
Mean single sequence MFE -35.08
Consensus MFE -26.25
Energy contribution -27.00
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.77
Structure conservation index 0.75
SVM decision value 0.49
SVM RNA-class probability 0.755636
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 90786 112 - 1281640
CAGGGUGUGUGUGAGUACUGUCGGCUCUCUGCAUUCGAAGCAGAGGAUCCAAUGCCGUGUUUACAUAUACAUGCAUAGUUACACG----UAUACAUAU----AUCUAUCUGAUGAGUAUC
((((..(((((((.(((((((.((.(((((((.......)))))))..)).((((.((((........))))))))....))).)----))).)))))----))...))))......... ( -31.20)
>DroSec_CAF1 36515 112 - 1
AAGGGUGUGUGUGAGUACUGUCGGCUCUCUGCAUUCGAAGCAUAGGAUCCGAUCCCGUGUUUACAUAUACAUGCAUAGUUAUACG----UAUACAUAU----AUCUAUCUUAUGAGUAUC
....((((((((((((((.(((((.(((.(((.......)))..))).)))))...))))))))))))))((((.(((.((((.(----....).)))----).)))((....)))))). ( -27.30)
>DroEre_CAF1 51151 120 - 1
CAGGGUGUGUGUGAGUAAUGUCGGCUCUCUGCAUUCGAAGCAGAGGAUCCGAUCCCGUGUUUACAUAUACAUGCAUAGGAGUACGUACGUGUACAUAUGCAUGUAUAGCUCAUGGGUAUC
...((((..(((((((...(((((.(((((((.......)))))))..)))))............((((((((((((...(((((....))))).)))))))))))))))))))..)))) ( -44.10)
>DroYak_CAF1 58938 114 - 1
CAGGGUGUGUGUGAGUACUGUCGGCUCUCUGCACUCGAAGCAGAGGAUCCGAUCCCGUGUUUACAUAUACAUGCAGCGGUGUACGCGUGUGUACAUA------UAUAUCUCAUGAAUGUC
..(((((((((((..(((.(((((.(((((((.......)))))))..)))))...)))........(((((((.(((.....))))))))))))))------))))))).......... ( -37.70)
>consensus
CAGGGUGUGUGUGAGUACUGUCGGCUCUCUGCAUUCGAAGCAGAGGAUCCGAUCCCGUGUUUACAUAUACAUGCAUAGGUAUACG____UAUACAUAU____AUAUAUCUCAUGAGUAUC
....((((((((((((((.(((((.(((((((.......)))))))..)))))...)))))))))))))).................................................. (-26.25 = -27.00 +   0.75)

alignment

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secondary structure

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dotplot

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Window 0

Location 90,818 – 90,938
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.28
Mean single sequence MFE -31.65
Consensus MFE -30.65
Energy contribution -31.40
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.88
Structure conservation index 0.97
SVM decision value 1.16
SVM RNA-class probability 0.924328
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 90818 120 - 1281640
UACAGAAAACUGUAUUUUCAGCAAAUAAAUAAACAAACAUCAGGGUGUGUGUGAGUACUGUCGGCUCUCUGCAUUCGAAGCAGAGGAUCCAAUGCCGUGUUUACAUAUACAUGCAUAGUU
(((((....)))))............................(.(((((((((...((...(((((((((((.......))))))).......)))).))...))))))))).)...... ( -30.91)
>DroSec_CAF1 36547 120 - 1
UACAGAAAACUGUAUUUUCAGCAAAUAAAUAAACAAACAUAAGGGUGUGUGUGAGUACUGUCGGCUCUCUGCAUUCGAAGCAUAGGAUCCGAUCCCGUGUUUACAUAUACAUGCAUAGUU
(((((....)))))......(((..............(....).((((((((((((((.(((((.(((.(((.......)))..))).)))))...)))))))))))))).)))...... ( -28.80)
>DroEre_CAF1 51191 120 - 1
UACAGAAAACUGUAUUUUCAGCAAAUAAAUAAACAAACAUCAGGGUGUGUGUGAGUAAUGUCGGCUCUCUGCAUUCGAAGCAGAGGAUCCGAUCCCGUGUUUACAUAUACAUGCAUAGGA
(((((....)))))......(((..............(....).(((((((((((((..(((((.(((((((.......)))))))..)))))....))))))))))))).)))...... ( -32.40)
>DroYak_CAF1 58972 120 - 1
UACAGAAAACUGUAUUUUCAGCAAAUAAACAAACAAACAUCAGGGUGUGUGUGAGUACUGUCGGCUCUCUGCACUCGAAGCAGAGGAUCCGAUCCCGUGUUUACAUAUACAUGCAGCGGU
(((((....)))))......(((..............(....).((((((((((((((.(((((.(((((((.......)))))))..)))))...)))))))))))))).)))...... ( -34.50)
>consensus
UACAGAAAACUGUAUUUUCAGCAAAUAAAUAAACAAACAUCAGGGUGUGUGUGAGUACUGUCGGCUCUCUGCAUUCGAAGCAGAGGAUCCGAUCCCGUGUUUACAUAUACAUGCAUAGGU
(((((....)))))......(((..............(....).((((((((((((((.(((((.(((((((.......)))))))..)))))...)))))))))))))).)))...... (-30.65 = -31.40 +   0.75)

alignment

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secondary structure

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dotplot

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Window 1

Location 90,898 – 91,015
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.25
Mean single sequence MFE -17.99
Consensus MFE -13.98
Energy contribution -14.97
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.02
Structure conservation index 0.78
SVM decision value 0.27
SVM RNA-class probability 0.661033
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 90898 117 - 1281640
GAAACAAGAUUGUGGUGUAUCAACAGGUAGAGACGAAAACGACAGAGUCUAAACAA---AAAUAUAUGCGUAAAACAGAAUACAGAAAACUGUAUUUUCAGCAAAUAAAUAAACAAACAU
.........((((.((((((......((..((((............))))..))..---....)))))).......(((((((((....)))))))))..))))................ ( -17.10)
>DroSec_CAF1 36627 117 - 1
AAAACAAGAUUGUGGUGUAUCAACAGGUAGAGACGAAAACGACAGAGUCUAAACAA---AAAUAUAUGCGUAAAACAGAAUACAGAAAACUGUAUUUUCAGCAAAUAAAUAAACAAACAU
.........((((.((((((......((..((((............))))..))..---....)))))).......(((((((((....)))))))))..))))................ ( -17.10)
>DroEre_CAF1 51271 116 - 1
GAGACAAGAUUAUGGCGUAUCAACAGGUAGAGACGGAAACGACA--GCCUAAACAAA--AAAUAUAUGCGUAAAACAGAAUACAGAAAACUGUAUUUUCAGCAAAUAAAUAAACAAACAU
.......(.(((.(((.((((....))))....((....))...--)))))).)...--...(((.(((.......(((((((((....)))))))))..))).)))............. ( -19.10)
>DroYak_CAF1 59052 118 - 1
GAGACGAGAUUGUGGCGUAUCAACAGGUAGAGACGGAAACGAAA--GUCUAAACAAAAAAAAUAUAUGCGUAAAACAGAAUACAGAAAACUGUAUUUUCAGCAAAUAAACAAACAAACAU
.........((((.((((((......((..(((((....)....--))))..)).........)))))).......(((((((((....)))))))))..))))................ ( -18.66)
>consensus
GAAACAAGAUUGUGGCGUAUCAACAGGUAGAGACGAAAACGACA__GUCUAAACAA___AAAUAUAUGCGUAAAACAGAAUACAGAAAACUGUAUUUUCAGCAAAUAAAUAAACAAACAU
......(((((.((...((((....))))....((....)).)).)))))............(((.(((.......(((((((((....)))))))))..))).)))............. (-13.98 = -14.97 +   1.00)

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 09:30:56 2006