Locus 1100

Sequence ID 2R_DroMel_CAF1
Location 4,414,260 – 4,414,402
Length 142
Max. P 0.993078
window1945 window1946 window1947 window1948

overview

Window 5

Location 4,414,260 – 4,414,380
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.50
Mean single sequence MFE -39.77
Consensus MFE -26.99
Energy contribution -28.10
Covariance contribution 1.11
Combinations/Pair 1.19
Mean z-score -2.83
Structure conservation index 0.68
SVM decision value 0.54
SVM RNA-class probability 0.775416
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4414260 120 + 20766785
CUAAGAUGAUGAAGUACAUCACGGAGCACGAGCAGGAGGACUACCUGCUCACCGGGUUCACCAGCCAGAAGGUGAAUCCCUUCCGCGAGAAGUCGUCCUGCACCGUUCUCUAAGGAGGCG
......(((((.....))))).((((.(((.((((((.((((.(.(((.....(((((((((........))))))))).....))).).)))).))))))..))).))))......... ( -46.00)
>DroVir_CAF1 1352 120 + 1
ACAAAAUGAAGAAAUAUAUAUCGGAGCACGAGCAGGAGGAUUACCUAUUGACUGGUUUCACCAGCCAGAAGGUAAAUCCCUUCCGCGAGAAAUCCUCGUGCACUGCUCUUUAAGCCGAUU
...................(((((.....((((((..(((((((((.(((.((((.....)))).))).)))).)))))....((((((.....))))))..))))))......))))). ( -41.90)
>DroGri_CAF1 1780 120 + 1
AUAAAAUGAAGAAAUAUAUAUCGGAGCACGAGCAGGAGGAUUAUCUAUUGACUGGUUUCACCAGCCAAAAGGUAAACCCCUUCCGUGAGAAGUCCUCGUGCACGGCUCUCUAAGCAGAUC
......................(((((.((.(((.(((((((((((.(((.((((.....)))).))).))))))....(((.(....))))))))).))).)))))))........... ( -38.40)
>DroWil_CAF1 1784 120 + 1
ACAAAAUGAUGAAAUAUAUCACAGAGCAUGAGCAGGAGGAUUAUCUAUUGACUGGUUUCACCAGCCAAAAGGUUAAUCCGUUCCGUGAGAAAUCCUCAUGCACAGUGCUUUAAGGCGGUC
......(((((.....))))).(((((((..((.((((((((((((.(((.((((.....)))).))).))).))))))..)))(((((.....)))))))...)))))))......... ( -34.70)
>DroMoj_CAF1 1696 120 + 1
AUAAAAUGAAGAAGUAUAUAUCGGAGCACGAGCAGGAGGAUUAUCUGUUGACUGGCUUCACCAGUCAGAAGGUAAACCCAUUCCGUGAGAAGUCGUCGUGCACUGCUCUUUAAGCAGGUU
.........................((((((...(((((.((((((.((((((((.....)))))))).)))))).))...)))..((....)).)))))).(((((.....)))))... ( -37.00)
>DroAna_CAF1 1946 120 + 1
CUAAAAUGAUGAAGUACAUCACGGAGCACGAGCAGGAGGACUACCUGCUGACUGGAUUCACCAGCCAGAAGGUUAAUCCCUUCCGCGAGAAGUCAUCAUGCACCGUACUUUAAGAUGGUG
.....(((((((..(...((.((((((....)).((.(((..((((.(((.((((.....)))).))).))))...))))))))).)).)..))))))).((((((........)))))) ( -40.60)
>consensus
AUAAAAUGAAGAAAUAUAUAACGGAGCACGAGCAGGAGGAUUACCUAUUGACUGGUUUCACCAGCCAGAAGGUAAAUCCCUUCCGCGAGAAGUCCUCGUGCACCGCUCUUUAAGCAGGUC
.....................(((.((((((((.((((((((((((.(((.((((.....)))).))).)))).)))))..)))))((....)).)))))).)))............... (-26.99 = -28.10 +   1.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 4,414,260 – 4,414,380
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.50
Mean single sequence MFE -41.18
Consensus MFE -27.07
Energy contribution -26.52
Covariance contribution -0.55
Combinations/Pair 1.26
Mean z-score -3.06
Structure conservation index 0.66
SVM decision value 0.59
SVM RNA-class probability 0.793253
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4414260 120 - 20766785
CGCCUCCUUAGAGAACGGUGCAGGACGACUUCUCGCGGAAGGGAUUCACCUUCUGGCUGGUGAACCCGGUGAGCAGGUAGUCCUCCUGCUCGUGCUCCGUGAUGUACUUCAUCAUCUUAG
..........(((.((((.((((((.((((.(..((....(((.((((((........))))))))).....))..).)))).)))))))))).))).((((((.....))))))..... ( -47.60)
>DroVir_CAF1 1352 120 - 1
AAUCGGCUUAAAGAGCAGUGCACGAGGAUUUCUCGCGGAAGGGAUUUACCUUCUGGCUGGUGAAACCAGUCAAUAGGUAAUCCUCCUGCUCGUGCUCCGAUAUAUAUUUCUUCAUUUUGU
.(((((......((((((.....(((((....((.(....).)).((((((..(((((((.....)))))))..))))))))))))))))).....)))))................... ( -43.90)
>DroGri_CAF1 1780 120 - 1
GAUCUGCUUAGAGAGCCGUGCACGAGGACUUCUCACGGAAGGGGUUUACCUUUUGGCUGGUGAAACCAGUCAAUAGAUAAUCCUCCUGCUCGUGCUCCGAUAUAUAUUUCUUCAUUUUAU
..........(.((((((.(((.(((((((((.....))))........((.((((((((.....)))))))).))....))))).))).)).)))))...................... ( -38.00)
>DroWil_CAF1 1784 120 - 1
GACCGCCUUAAAGCACUGUGCAUGAGGAUUUCUCACGGAACGGAUUAACCUUUUGGCUGGUGAAACCAGUCAAUAGAUAAUCCUCCUGCUCAUGCUCUGUGAUAUAUUUCAUCAUUUUGU
.............(((.(.(((((((((....))..(((..((((((..((.((((((((.....)))))))).)).)))))))))..))))))).).)))................... ( -35.70)
>DroMoj_CAF1 1696 120 - 1
AACCUGCUUAAAGAGCAGUGCACGACGACUUCUCACGGAAUGGGUUUACCUUCUGACUGGUGAAGCCAGUCAACAGAUAAUCCUCCUGCUCGUGCUCCGAUAUAUACUUCUUCAUUUUAU
...((((((...)))))).(((((((((....))..(((..(((((...((..(((((((.....)))))))..))..)))))))).).))))))......................... ( -32.90)
>DroAna_CAF1 1946 120 - 1
CACCAUCUUAAAGUACGGUGCAUGAUGACUUCUCGCGGAAGGGAUUAACCUUCUGGCUGGUGAAUCCAGUCAGCAGGUAGUCCUCCUGCUCGUGCUCCGUGAUGUACUUCAUCAUUUUAG
........((((((((((.((((((.((....))((((..(((((((.(((.((((((((.....)))))))).)))))))))).)))))))))).))))((((.....)))))))))). ( -49.00)
>consensus
AACCUGCUUAAAGAACAGUGCACGAGGACUUCUCACGGAAGGGAUUUACCUUCUGGCUGGUGAAACCAGUCAACAGAUAAUCCUCCUGCUCGUGCUCCGAGAUAUACUUCAUCAUUUUAU
.................(.((((((.((....))..(((..(((((...((.((((((((.....)))))))).))..))))))))...)))))).)....................... (-27.07 = -26.52 +  -0.55)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 4,414,300 – 4,414,402
Length 102
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 72.14
Mean single sequence MFE -31.13
Consensus MFE -13.77
Energy contribution -13.97
Covariance contribution 0.20
Combinations/Pair 1.36
Mean z-score -2.60
Structure conservation index 0.44
SVM decision value 2.37
SVM RNA-class probability 0.993078
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4414300 102 + 20766785
CUACCUGCUCACCGGGUUCACCAGCCAGAAGGUGAAUCCCUUCCGCGAGAAGUCGUCCUGCACCGUUCUCUAAGGAGGCGGUG-AGGAUGGUCCGCCGUUGCC
......((.....(((((((((........))))))))).....(((.((..(((((((.((((((.(((....)))))))))-))))))))))))....)). ( -41.50)
>DroVir_CAF1 1392 86 + 1
UUACCUAUUGACUGGUUUCACCAGCCAGAAGGUAAAUCCCUUCCGCGAGAAAUCCUCGUGCACUGCUCUUUAAGCCGAUUC--------GAAUC---------
((((((.(((.((((.....)))).))).))))))........((((((.....))))))..(.(((.....))).)....--------.....--------- ( -23.20)
>DroPse_CAF1 2555 83 + 1
UUACCUUUUGACUGGAUUCACCAGCCAGAAGGUAAAUCCAUUCCGUGAAAAGUCUUCAUGCACCGUUCUUUAAGGAGGAGUUU--------------------
((((((((((.((((.....)))).)))))))))).(((....((((((.....))))))..((.........)).)))....-------------------- ( -25.70)
>DroSim_CAF1 1825 102 + 1
UUACCUGCUUACCGGAUUCACCAGCCAGAAGGUGAAUCCCUUCCGCGAGAAAUCGUCGUGCACAGUCCUCUAAGGAGGCGGUG-AGGAUUGUCCGCCGUUGCC
......((..((.(((((((((........))))))))).....((((....)))).(((.(((((((((...(....)...)-)))))))).))).)).)). ( -35.90)
>DroMoj_CAF1 1736 94 + 1
UUAUCUGUUGACUGGCUUCACCAGUCAGAAGGUAAACCCAUUCCGUGAGAAGUCGUCGUGCACUGCUCUUUAAGCAGGUUUUUAUGGAUGGAUC---------
((((((.((((((((.....)))))))).))))))..((((.(((((((((((......)).(((((.....))))).)))))))))))))...--------- ( -34.80)
>DroPer_CAF1 2662 83 + 1
UUACCUUUUGACUGGAUUCACCAGCCAGAAGGUAAAUCCAUUCCGUGAAAAGUCUUCAUGCACCGUUCUUUAAGGAGGAGUUU--------------------
((((((((((.((((.....)))).)))))))))).(((....((((((.....))))))..((.........)).)))....-------------------- ( -25.70)
>consensus
UUACCUGUUGACUGGAUUCACCAGCCAGAAGGUAAAUCCAUUCCGCGAGAAGUCGUCGUGCACCGUUCUUUAAGGAGGAGUUU______GG__C_________
((((((.(((.((((.....)))).))).))))))........(((((.......)))))......((((....))))......................... (-13.77 = -13.97 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 4,414,300 – 4,414,402
Length 102
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 72.14
Mean single sequence MFE -28.92
Consensus MFE -16.22
Energy contribution -16.17
Covariance contribution -0.05
Combinations/Pair 1.35
Mean z-score -1.70
Structure conservation index 0.56
SVM decision value 0.90
SVM RNA-class probability 0.878669
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4414300 102 - 20766785
GGCAACGGCGGACCAUCCU-CACCGCCUCCUUAGAGAACGGUGCAGGACGACUUCUCGCGGAAGGGAUUCACCUUCUGGCUGGUGAACCCGGUGAGCAGGUAG
(....)((....)).((((-(((((.(((....)))..))))).))))..(((((((((....(((.((((((........))))))))).))))).)))).. ( -38.70)
>DroVir_CAF1 1392 86 - 1
---------GAUUC--------GAAUCGGCUUAAAGAGCAGUGCACGAGGAUUUCUCGCGGAAGGGAUUUACCUUCUGGCUGGUGAAACCAGUCAAUAGGUAA
---------.....--------(((((.((((...))))....(.((((.....)))).).....)))))((((..(((((((.....)))))))..)))).. ( -26.10)
>DroPse_CAF1 2555 83 - 1
--------------------AAACUCCUCCUUAAAGAACGGUGCAUGAAGACUUUUCACGGAAUGGAUUUACCUUCUGGCUGGUGAAUCCAGUCAAAAGGUAA
--------------------....((((((.....(((.(((........))).)))..)))..))).(((((((.(((((((.....))))))).))))))) ( -23.80)
>DroSim_CAF1 1825 102 - 1
GGCAACGGCGGACAAUCCU-CACCGCCUCCUUAGAGGACUGUGCACGACGAUUUCUCGCGGAAGGGAUUCACCUUCUGGCUGGUGAAUCCGGUAAGCAGGUAA
(....)(((((........-..)))))(((.....)))((((...((.(((....)))))....(((((((((........))))))))).....)))).... ( -34.90)
>DroMoj_CAF1 1736 94 - 1
---------GAUCCAUCCAUAAAAACCUGCUUAAAGAGCAGUGCACGACGACUUCUCACGGAAUGGGUUUACCUUCUGACUGGUGAAGCCAGUCAACAGAUAA
---------(((((((((........((((((...)))))).....((.(....)))..)).)))))))...((..(((((((.....)))))))..)).... ( -26.20)
>DroPer_CAF1 2662 83 - 1
--------------------AAACUCCUCCUUAAAGAACGGUGCAUGAAGACUUUUCACGGAAUGGAUUUACCUUCUGGCUGGUGAAUCCAGUCAAAAGGUAA
--------------------....((((((.....(((.(((........))).)))..)))..))).(((((((.(((((((.....))))))).))))))) ( -23.80)
>consensus
_________G__CC______AAACACCUCCUUAAAGAACGGUGCACGACGACUUCUCACGGAAGGGAUUUACCUUCUGGCUGGUGAAUCCAGUCAACAGGUAA
.........................((...((...(((.(((........))).)))...))..))..((((((..(((((((.....)))))))..)))))) (-16.22 = -16.17 +  -0.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:33 2006