Locus 5388

Sequence ID X_DroMel_CAF1
Location 14,010,063 – 14,010,251
Length 188
Max. P 0.964322
window8742 window8743 window8744 window8745

overview

Window 2

Location 14,010,063 – 14,010,177
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.17
Mean single sequence MFE -26.34
Consensus MFE -18.18
Energy contribution -17.58
Covariance contribution -0.60
Combinations/Pair 1.12
Mean z-score -1.67
Structure conservation index 0.69
SVM decision value -0.04
SVM RNA-class probability 0.513582
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14010063 114 + 22224390
ACA---UACAUCAAUGUUUUAACUAAGUAUUAGCGUUAAAAAAUAUAAUAUAAAGCUUUAAUUAAGU---UGGGCUUUUUAUAAACAGCUUGCAGCUUUGAUUAAACUUGGAAGCUGCGA
...---..........(((((((...........)))))))......(((.(((((((.........---.))))))).))).......((((((((((.(.......).)))))))))) ( -21.20)
>DroSec_CAF1 36743 114 + 1
ACA---UGAAUCAAUGUUUGAACUAAGUAUUAGCGUUAGCAAAUAUAAUAUAAAGCUUUUAUUAAGU---UGGGCUUUUUAUAAACAGCUUGCAGCUUUGAUUAAACUUGGAAACUGCGA
...---....((((.((((((.....(((((.((....)).)))))....(((((((.....(((((---((.............))))))).))))))).))))))))))......... ( -20.22)
>DroSim_CAF1 38180 114 + 1
ACA---CGAAUCAAUGUUUUAACUAAGUAUUAGCGUUAGCAAAUAUAAUAUAAAGCUUUGAUUAAGU---UGGGCUUUUUAUGAACAGCUUGCAGCUUUGAUUAAACUUGGAAGCUGCGA
...---..((((((.((((((.....(((((.((....)).)))))....)))))).))))))((((---((..(.......)..))))))((((((((.(.......).)))))))).. ( -31.60)
>DroEre_CAF1 34717 114 + 1
ACA---CGCAUCAAUGU-UAAAAAAACGAUUAGCGCUA--CAAUGUAAUGUGAAGCUUUGAUUAAGCCGCUGGGCUUUUUAUGAACAGCUUGCAGCUUUGAUGAAACUUGGAAGCUGCGA
...---(((((....((-(((........)))))((..--....)).)))))(((((((.((.(((((....)))))...)).)).)))))((((((((.(.......).)))))))).. ( -29.50)
>DroYak_CAF1 37474 118 + 1
ACAAUAAGCAUCGAUUUUUUAAAUAACGAUUAGCGCUA--AAAUGUAAUAAAAAGCUUUGAUUAAGUCGCUGGGCUUUUUAUGAGCAGCUUGCAGCUUUGAUUAAACUUGGAAGCUGCGA
.....((((((((.((........))))))....(((.--.......(((((((((((((((...))))..))))))))))).))).))))((((((((.(.......).)))))))).. ( -29.20)
>consensus
ACA___CGCAUCAAUGUUUUAACUAAGUAUUAGCGUUA__AAAUAUAAUAUAAAGCUUUGAUUAAGU___UGGGCUUUUUAUGAACAGCUUGCAGCUUUGAUUAAACUUGGAAGCUGCGA
...............................(((((........)).(((.(((((((.............))))))).))).....)))(((((((((.(.......).))))))))). (-18.18 = -17.58 +  -0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 14,010,100 – 14,010,212
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.41
Mean single sequence MFE -27.06
Consensus MFE -22.32
Energy contribution -21.72
Covariance contribution -0.60
Combinations/Pair 1.14
Mean z-score -2.04
Structure conservation index 0.82
SVM decision value 1.57
SVM RNA-class probability 0.964322
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14010100 112 + 22224390
AAAUAUAAUAUAAAGCUUUAAUUAAGU---UGGGCUUUUUAUAAACAGCUUGCAGCUUUGAUUAAACUUGGAAGCUGCGACUAUUUUAAGCAUUU-UCAAAGAGCUUUUAGUUUAA----
.....(((...((((((((....((((---...((((.....(((.((.((((((((((.(.......).)))))))))))).))).))))))))-....))))))))....))).---- ( -24.20)
>DroSec_CAF1 36780 113 + 1
AAAUAUAAUAUAAAGCUUUUAUUAAGU---UGGGCUUUUUAUAAACAGCUUGCAGCUUUGAUUAAACUUGGAAACUGCGACUAUUUUAAGCAUUUUUCCAAGAGCUUUUAGUUUAA----
.....(((...((((((((((..((((---((((((.((....)).))))..))))))....))))((((((((.(((...........)))..))))))))))))))....))).---- ( -23.20)
>DroSim_CAF1 38217 112 + 1
AAAUAUAAUAUAAAGCUUUGAUUAAGU---UGGGCUUUUUAUGAACAGCUUGCAGCUUUGAUUAAACUUGGAAGCUGCGACUAUUUUAAGCAUUU-UGCAAGAGCUUUUAGUUUAA----
.....(((...((((((((....((((---((..(.......)..))))))((((((((.(.......).))))))))...........((....-.)).))))))))....))).---- ( -27.60)
>DroEre_CAF1 34751 115 + 1
CAAUGUAAUGUGAAGCUUUGAUUAAGCCGCUGGGCUUUUUAUGAACAGCUUGCAGCUUUGAUGAAACUUGGAAGCUGCGACUAUUUCAAGCAUUU-UCCAAAAGCUUUUAGUGUAA----
...........((((((((((..(.((.((((..(.......)..))))((((((((((.(.......).)))))))))).........)).)..-))..))))))))........---- ( -29.20)
>DroYak_CAF1 37512 119 + 1
AAAUGUAAUAAAAAGCUUUGAUUAAGUCGCUGGGCUUUUUAUGAGCAGCUUGCAGCUUUGAUUAAACUUGGAAGCUGCGACUAUUUUAAGCAUAU-UCCAAAAGCUUUUGGUUUAGUUUU
..............((((.((...(((((((..((((.....)))))))..((((((((.(.......).))))))))))))..)).)))).((.-.(((((....)))))..))..... ( -31.10)
>consensus
AAAUAUAAUAUAAAGCUUUGAUUAAGU___UGGGCUUUUUAUGAACAGCUUGCAGCUUUGAUUAAACUUGGAAGCUGCGACUAUUUUAAGCAUUU_UCCAAGAGCUUUUAGUUUAA____
...........((((((((..............((((.....(((.((.((((((((((.(.......).)))))))))))).))).)))).........))))))))............ (-22.32 = -21.72 +  -0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 14,010,100 – 14,010,212
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.41
Mean single sequence MFE -21.39
Consensus MFE -15.98
Energy contribution -15.86
Covariance contribution -0.12
Combinations/Pair 1.10
Mean z-score -2.08
Structure conservation index 0.75
SVM decision value 0.74
SVM RNA-class probability 0.839319
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14010100 112 - 22224390
----UUAAACUAAAAGCUCUUUGA-AAAUGCUUAAAAUAGUCGCAGCUUCCAAGUUUAAUCAAAGCUGCAAGCUGUUUAUAAAAAGCCCA---ACUUAAUUAAAGCUUUAUAUUAUAUUU
----........((((((..((((-....((((.(((((((.(((((((.............)))))))..))))))).....))))...---..))))....))))))........... ( -19.92)
>DroSec_CAF1 36780 113 - 1
----UUAAACUAAAAGCUCUUGGAAAAAUGCUUAAAAUAGUCGCAGUUUCCAAGUUUAAUCAAAGCUGCAAGCUGUUUAUAAAAAGCCCA---ACUUAAUAAAAGCUUUAUAUUAUAUUU
----........((((((.(((.......((((.(((((((.(((((((.............)))))))..))))))).....))))...---......))).))))))........... ( -18.21)
>DroSim_CAF1 38217 112 - 1
----UUAAACUAAAAGCUCUUGCA-AAAUGCUUAAAAUAGUCGCAGCUUCCAAGUUUAAUCAAAGCUGCAAGCUGUUCAUAAAAAGCCCA---ACUUAAUCAAAGCUUUAUAUUAUAUUU
----........((((((...((.-....))....((((((.(((((((.............)))))))..)))))).............---..........))))))........... ( -18.12)
>DroEre_CAF1 34751 115 - 1
----UUACACUAAAAGCUUUUGGA-AAAUGCUUGAAAUAGUCGCAGCUUCCAAGUUUCAUCAAAGCUGCAAGCUGUUCAUAAAAAGCCCAGCGGCUUAAUCAAAGCUUCACAUUACAUUG
----.........(((((((((((-(..(((...........)))..)))))..........(((((((..(((..........)))...)))))))....)))))))............ ( -25.50)
>DroYak_CAF1 37512 119 - 1
AAAACUAAACCAAAAGCUUUUGGA-AUAUGCUUAAAAUAGUCGCAGCUUCCAAGUUUAAUCAAAGCUGCAAGCUGCUCAUAAAAAGCCCAGCGACUUAAUCAAAGCUUUUUAUUACAUUU
.........(((((....)))))(-(((.((((.....(((((((((((...(((((.....)))))..)))))(((.......)))...))))))......))))....))))...... ( -25.20)
>consensus
____UUAAACUAAAAGCUCUUGGA_AAAUGCUUAAAAUAGUCGCAGCUUCCAAGUUUAAUCAAAGCUGCAAGCUGUUCAUAAAAAGCCCA___ACUUAAUCAAAGCUUUAUAUUAUAUUU
............((((((...........(((......))).(((((((...(((((.....)))))..)))))))...........................))))))........... (-15.98 = -15.86 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 14,010,137 – 14,010,251
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.40
Mean single sequence MFE -25.08
Consensus MFE -18.56
Energy contribution -19.16
Covariance contribution 0.60
Combinations/Pair 1.11
Mean z-score -1.63
Structure conservation index 0.74
SVM decision value 0.10
SVM RNA-class probability 0.584894
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14010137 114 + 22224390
AUAAACAGCUUGCAGCUUUGAUUAAACUUGGAAGCUGCGACUAUUUUAAGCAUUU-UCAAAGAGCUUUUAGUUUAA-----AUAUAGCAUGAAACUUUAUGGUUUUCCUAGUUUUAACAC
.......(((.((((((((.(.......).))))))))(((((....((((....-.......)))).)))))...-----....))).(((((((....((....)).))))))).... ( -25.60)
>DroSec_CAF1 36817 115 + 1
AUAAACAGCUUGCAGCUUUGAUUAAACUUGGAAACUGCGACUAUUUUAAGCAUUUUUCCAAGAGCUUUUAGUUUAA-----AUAUAGCAUGCAACUUUAGGGUUUUCCUAUUUUAAUAAC
......((.((((((((..(((((((((((((((.(((...........)))..))))))))....)))))))...-----....))).))))))).((((.....)))).......... ( -22.70)
>DroSim_CAF1 38254 114 + 1
AUGAACAGCUUGCAGCUUUGAUUAAACUUGGAAGCUGCGACUAUUUUAAGCAUUU-UGCAAGAGCUUUUAGUUUAA-----AUAUAGCAUGAAACUUUAGGGUUUUCCUAUUUUAAUUAC
.((((.(((((((((((((.(.......).))))))))...........((....-.))..)))))))))..((((-----(.((((...((((((....)))))).))))))))).... ( -24.70)
>DroEre_CAF1 34791 114 + 1
AUGAACAGCUUGCAGCUUUGAUGAAACUUGGAAGCUGCGACUAUUUCAAGCAUUU-UCCAAAAGCUUUUAGUGUAA-----AUGUAGCAUAAAACUUGAUAGUUUCCUUAGCUUCAACAC
.(((..((((.((((((((.(.......).))))))))(((((((..((((....-.......))))...((((..-----.....)))).......))))))).....))))))).... ( -23.40)
>DroYak_CAF1 37552 119 + 1
AUGAGCAGCUUGCAGCUUUGAUUAAACUUGGAAGCUGCGACUAUUUUAAGCAUAU-UCCAAAAGCUUUUGGUUUAGUUUUAGCUUAGCAUAAAACUUGAAUGUUUUCUUAGUUUAGACUC
.(((((((.((((((((((.(.......).)))))))))))).....((((.((.-.(((((....)))))..))))))..))))).....(((((.(((....)))..)))))...... ( -29.00)
>consensus
AUGAACAGCUUGCAGCUUUGAUUAAACUUGGAAGCUGCGACUAUUUUAAGCAUUU_UCCAAGAGCUUUUAGUUUAA_____AUAUAGCAUGAAACUUUAGGGUUUUCCUAGUUUAAACAC
.......(((.((((((((.(.......).))))))))(((((....((((............)))).)))))............)))..((((((....)))))).............. (-18.56 = -19.16 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:47 2006