Locus 6043

Sequence ID 2R_DroMel_CAF1
Location 19,010,884 – 19,011,043
Length 159
Max. P 0.999681
window9684 window9685 window9686 window9687

overview

Window 4

Location 19,010,884 – 19,011,003
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 73.01
Mean single sequence MFE -35.47
Consensus MFE -27.44
Energy contribution -29.67
Covariance contribution 2.23
Combinations/Pair 1.14
Mean z-score -2.18
Structure conservation index 0.77
SVM decision value 3.88
SVM RNA-class probability 0.999681
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19010884 119 + 20766785
CUGUAAAAUCCUGUAAAAGAGUACAAAGACUUAUA-AAUAAAUAGGAUGAGUUCCUUCGCCCGGGUUCCCAGCACACCUCCUCCUUCGUAUGAGGAGGCAAUGGGCUGGGAAACACGGAG
.......(((((((....((((......))))...-.....)))))))............(((..((((((((.(((((((((........)))))))...)).))))))))...))).. ( -39.10)
>DroSec_CAF1 109144 112 + 1
-------AGCCUGUAGAAGAGUACAAAGACUUAUA-AAUAAAAAGCAUGAGUUCCUUCGCCAUGGUUCCCAGCACACCUCCUCCUUCGUAUGAGGAGGCAAUGGGCUGGACGCCACGGAU
-------........((((.(......(((((((.-..........)))))))))))).((.((((..(((((.(((((((((........)))))))...)).)))))..)))).)).. ( -33.90)
>DroYak_CAF1 113126 98 + 1
----------------------ACUAAGACUGAAAGAGUAAAUAACAUGAGUUCCUACGCCCAGGUGUCCAGCACACCCCCGCCUUCGUAUGAGGAGGCCAUGGGCUGGGCACCUCACAG
----------------------.......(((.....(((...(((....)))..)))....(((((((((((...((...((((((......))))))...)))))))))))))..))) ( -33.40)
>consensus
_______A_CCUGUA_AAGAGUACAAAGACUUAUA_AAUAAAUAGCAUGAGUUCCUUCGCCCAGGUUCCCAGCACACCUCCUCCUUCGUAUGAGGAGGCAAUGGGCUGGGCACCACGGAG
...........................(((((((............)))))))......((.(((((((((((.((...(((((((.....)))))))...)).))))))))))).)).. (-27.44 = -29.67 +   2.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 19,010,884 – 19,011,003
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 73.01
Mean single sequence MFE -37.80
Consensus MFE -28.55
Energy contribution -29.67
Covariance contribution 1.12
Combinations/Pair 1.17
Mean z-score -2.14
Structure conservation index 0.76
SVM decision value 3.67
SVM RNA-class probability 0.999515
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19010884 119 - 20766785
CUCCGUGUUUCCCAGCCCAUUGCCUCCUCAUACGAAGGAGGAGGUGUGCUGGGAACCCGGGCGAAGGAACUCAUCCUAUUUAUU-UAUAAGUCUUUGUACUCUUUUACAGGAUUUUACAG
.((((.(.((((((((.(((..(((((((....).))))))..))).)))))))).)))))...((((.....)))).......-...(((((((.(((......))))))))))..... ( -41.60)
>DroSec_CAF1 109144 112 - 1
AUCCGUGGCGUCCAGCCCAUUGCCUCCUCAUACGAAGGAGGAGGUGUGCUGGGAACCAUGGCGAAGGAACUCAUGCUUUUUAUU-UAUAAGUCUUUGUACUCUUCUACAGGCU-------
..((((((..((((((.(((..(((((((....).))))))..))).))))))..)))))).(((((.((....((((......-...))))....)).).))))........------- ( -39.90)
>DroYak_CAF1 113126 98 - 1
CUGUGAGGUGCCCAGCCCAUGGCCUCCUCAUACGAAGGCGGGGGUGUGCUGGACACCUGGGCGUAGGAACUCAUGUUAUUUACUCUUUCAGUCUUAGU----------------------
(((.((((.(((((((((...((((.(......).)))).)))((((.....))))))))))((((((((....))).))))))))).))).......---------------------- ( -31.90)
>consensus
CUCCGUGGUGCCCAGCCCAUUGCCUCCUCAUACGAAGGAGGAGGUGUGCUGGGAACCAGGGCGAAGGAACUCAUGCUAUUUAUU_UAUAAGUCUUUGUACUCUU_UACAGG_U_______
..((.(((((((((((.(((..(((((((....).))))))..))).))))))))))).))..(((((.((..................)))))))........................ (-28.55 = -29.67 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 19,010,923 – 19,011,043
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 77.36
Mean single sequence MFE -42.60
Consensus MFE -29.26
Energy contribution -30.95
Covariance contribution 1.69
Combinations/Pair 1.27
Mean z-score -1.87
Structure conservation index 0.69
SVM decision value 0.95
SVM RNA-class probability 0.887433
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19010923 120 + 20766785
AAUAGGAUGAGUUCCUUCGCCCGGGUUCCCAGCACACCUCCUCCUUCGUAUGAGGAGGCAAUGGGCUGGGAAACACGGAGAUCACACAGCACCACGUGGCUGCUCGCGGAGAAUACCUCA
.......((((...(((((((((..((((((((.(((((((((........)))))))...)).))))))))...))).........((((((....)).)))).)))))).....)))) ( -48.30)
>DroSec_CAF1 109176 120 + 1
AAAAGCAUGAGUUCCUUCGCCAUGGUUCCCAGCACACCUCCUCCUUCGUAUGAGGAGGCAAUGGGCUGGACGCCACGGAUAUCACACAGCACCACGCGGCUACUCCCGGAGAAUUCUUCA
........((((((.((((((.((((..(((((.(((((((((........)))))))...)).)))))..)))).)).........(((........))).....)))))))))).... ( -39.60)
>DroEre_CAF1 111263 119 + 1
-CAAAAAUGAGUUCCUUCGACCACGUUUCCAGCACACCACCACCUUCCUAUGAGGAGGCCAUGGGCUGGCGACCUCGCAGCUCGCAGAGCACCGCGAUGCUGUUCCCGCAGGGCAACCCU
-.........(((((((((.....(((.(((((...(((...(((((......)))))...)))))))).)))...(((((((((........)))).)))))...)).)))).)))... ( -36.60)
>DroYak_CAF1 113144 120 + 1
AAUAACAUGAGUUCCUACGCCCAGGUGUCCAGCACACCCCCGCCUUCGUAUGAGGAGGCCAUGGGCUGGGCACCUCACAGAUCGCUGAGCACCAGGACGCUGCUCCCGCGGAAUACAUCU
......(((.(((((.......(((((((((((...((...((((((......))))))...)))))))))))))........((.(((((.(.....).)))))..))))))).))).. ( -45.90)
>consensus
AAAAACAUGAGUUCCUUCGCCCAGGUUCCCAGCACACCUCCUCCUUCGUAUGAGGAGGCAAUGGGCUGGGCACCACGCAGAUCACACAGCACCACGAGGCUGCUCCCGCAGAAUACCUCA
..........((((.((((((.(((((((((((.((...(((((((.....)))))))...)).))))))))))).)).........(((........))).....))))))))...... (-29.26 = -30.95 +   1.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 19,010,923 – 19,011,043
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.36
Mean single sequence MFE -49.35
Consensus MFE -33.06
Energy contribution -36.12
Covariance contribution 3.06
Combinations/Pair 1.21
Mean z-score -1.63
Structure conservation index 0.67
SVM decision value 0.19
SVM RNA-class probability 0.628223
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19010923 120 - 20766785
UGAGGUAUUCUCCGCGAGCAGCCACGUGGUGCUGUGUGAUCUCCGUGUUUCCCAGCCCAUUGCCUCCUCAUACGAAGGAGGAGGUGUGCUGGGAACCCGGGCGAAGGAACUCAUCCUAUU
((((...((((.(((.((((.((....)))))).........(((.(.((((((((.(((..(((((((....).))))))..))).)))))))).))))))).)))).))))....... ( -51.20)
>DroSec_CAF1 109176 120 - 1
UGAAGAAUUCUCCGGGAGUAGCCGCGUGGUGCUGUGUGAUAUCCGUGGCGUCCAGCCCAUUGCCUCCUCAUACGAAGGAGGAGGUGUGCUGGGAACCAUGGCGAAGGAACUCAUGCUUUU
(((....(((.(((((....((((((.(((((.....).)))))))))).((((((.(((..(((((((....).))))))..))).))))))..)).))).))).....)))....... ( -45.30)
>DroEre_CAF1 111263 119 - 1
AGGGUUGCCCUGCGGGAACAGCAUCGCGGUGCUCUGCGAGCUGCGAGGUCGCCAGCCCAUGGCCUCCUCAUAGGAAGGUGGUGGUGUGCUGGAAACGUGGUCGAAGGAACUCAUUUUUG-
.(((((..(((.(((...((((.((((((....))))))))))(.(.((..(((((((((.((((((.....)).)))).))))...)))))..)).).)))).)))))))).......- ( -49.30)
>DroYak_CAF1 113144 120 - 1
AGAUGUAUUCCGCGGGAGCAGCGUCCUGGUGCUCAGCGAUCUGUGAGGUGCCCAGCCCAUGGCCUCCUCAUACGAAGGCGGGGGUGUGCUGGACACCUGGGCGUAGGAACUCAUGUUAUU
..(((..((((((....)).((((((.((((..(((((((((((((((.(.(((.....))).).)))))).((....)).)))).)))))..)))).)))))).))))..)))...... ( -51.60)
>consensus
AGAGGUAUUCUCCGGGAGCAGCCUCGUGGUGCUCUGCGAUCUCCGAGGUGCCCAGCCCAUGGCCUCCUCAUACGAAGGAGGAGGUGUGCUGGAAACCUGGGCGAAGGAACUCAUGCUAUU
.(((...((((.((.(((((.(.....).)))))........((.(((((((((((.(((..(((((((....).))))))..))).))))))))))).)))).)))).)))........ (-33.06 = -36.12 +   3.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:01:08 2006