Locus 1288

Sequence ID 2L_DroMel_CAF1
Location 3,416,522 – 3,416,621
Length 99
Max. P 0.992898
window2100 window2101

overview

Window 0

Location 3,416,522 – 3,416,621
Length 99
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 74.07
Mean single sequence MFE -27.25
Consensus MFE -15.97
Energy contribution -17.17
Covariance contribution 1.20
Combinations/Pair 1.05
Mean z-score -2.04
Structure conservation index 0.59
SVM decision value 1.62
SVM RNA-class probability 0.968327
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3416522 99 + 22407834
GAAAGUGGUCCGCAGGCAACUGCCAA-AAA--UAUGGGCGAUAGCGAUGCCAGCGUGACCGGUUUGUAUAA---GAUAUGAUAUCAUGCGAACAUAAA-CUUAUUU--------------
..(((((((((((.((((....(((.-...--..)))((....))..)))).))).)))).((((((((..---((((...))))))))))))....)-)))....-------------- ( -31.10)
>DroSec_CAF1 5459 99 + 1
GAAAGUGGUCCGCAGGCAACUACCAAAAAA--UAUGGGCGAUAGAGAUGCCAGCGUGACCGGUUUGUAUAA---GAAAA-AAAUCUUCAGAUUCCAAA-AUGAUAU--------------
.(((.((((((((.((((.((.(((.....--..))).......)).)))).))).))))).)))((((..---.....-.((((....)))).....-...))))-------------- ( -22.79)
>DroAna_CAF1 7899 90 + 1
GAAAGUGGCCCAAAGGCAACUACCAA-AAAAGUAUUGUCGAUAGCGGUGGUAGCGUGACCGGUUUGUACACUGAGAAAG-AAA-------------AG-GUUAUCU--------------
...(((.(((....))).))).....-.....(((..(((....)))..)))..((((((..(((...(.....)...)-)).-------------.)-)))))..-------------- ( -16.90)
>DroSim_CAF1 5688 98 + 1
GAAAGUGGUCCGCAGGCAACUACCAA-AAA--UAUGGGCGAUAGCGAUGCCAGCGUGACCGGUUUGUAUAA---GAAAC-AAAUCUUCAGAUUCCAAA-AUGAUAU--------------
(((...(((((((.((((....(((.-...--..)))((....))..)))).))).))))(((((((....---...))-))))))))..........-.......-------------- ( -28.30)
>DroEre_CAF1 5601 113 + 1
GAAAGUGGUCGGCAGGCAACUACCAA-AAA--UAUGGGCGAUAGCGAUGCCCGCGUGACCGGUUUGUAUAC---GAGCA-AAAUCUUCAGAUACCACAAAUGAUAUCACGAAGAGCAGCU
.(((.((((((((.((((....(((.-...--..)))((....))..)))).)).)))))).)))......---.(((.-...(((((.((((.((....)).))))..)))))...))) ( -32.40)
>DroYak_CAF1 6089 101 + 1
GAAAGUGGUCCGCAGGCAACUACCAA-AAA--UAUGGGCGAUAGCGAUGCCAGCGUGACCGGUUUGUAUAC---AAACA-AAAUUUUCAGAUGCCAAA------------AAGAGCAGCU
(((((((((((((.((((....(((.-...--..)))((....))..)))).))).)))).(((((....)---)))).-..))))))((.(((....------------....))).)) ( -32.00)
>consensus
GAAAGUGGUCCGCAGGCAACUACCAA_AAA__UAUGGGCGAUAGCGAUGCCAGCGUGACCGGUUUGUAUAA___GAAAA_AAAUCUUCAGAUUCCAAA_AUGAUAU______________
.(((.((((((((.((((....(((.........)))((....))..)))).))).))))).)))....................................................... (-15.97 = -17.17 +   1.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 3,416,522 – 3,416,621
Length 99
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.07
Mean single sequence MFE -27.03
Consensus MFE -18.73
Energy contribution -19.45
Covariance contribution 0.72
Combinations/Pair 1.11
Mean z-score -2.44
Structure conservation index 0.69
SVM decision value 2.36
SVM RNA-class probability 0.992898
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3416522 99 - 22407834
--------------AAAUAAG-UUUAUGUUCGCAUGAUAUCAUAUC---UUAUACAAACCGGUCACGCUGGCAUCGCUAUCGCCCAUA--UUU-UUGGCAGUUGCCUGCGGACCACUUUC
--------------..(((((-..((((.((....))...)))).)---)))).......((((.(((.((((..((((.........--...-.))))...)))).)))))))...... ( -26.42)
>DroSec_CAF1 5459 99 - 1
--------------AUAUCAU-UUUGGAAUCUGAAGAUUU-UUUUC---UUAUACAAACCGGUCACGCUGGCAUCUCUAUCGCCCAUA--UUUUUUGGUAGUUGCCUGCGGACCACUUUC
--------------.......-...((......((((...-...))---)).......))((((.(((.((((...((((((......--.....)))))).)))).)))))))...... ( -26.12)
>DroAna_CAF1 7899 90 - 1
--------------AGAUAAC-CU-------------UUU-CUUUCUCAGUGUACAAACCGGUCACGCUACCACCGCUAUCGACAAUACUUUU-UUGGUAGUUGCCUUUGGGCCACUUUC
--------------.......-..-------------...-.......(((((((......)).)))))......((((((((.((....)).-)))))))).(((....)))....... ( -14.20)
>DroSim_CAF1 5688 98 - 1
--------------AUAUCAU-UUUGGAAUCUGAAGAUUU-GUUUC---UUAUACAAACCGGUCACGCUGGCAUCGCUAUCGCCCAUA--UUU-UUGGUAGUUGCCUGCGGACCACUUUC
--------------.......-...((......((((...-...))---)).......))((((.(((.((((..(((((((......--...-.))))))))))).)))))))...... ( -26.92)
>DroEre_CAF1 5601 113 - 1
AGCUGCUCUUCGUGAUAUCAUUUGUGGUAUCUGAAGAUUU-UGCUC---GUAUACAAACCGGUCACGCGGGCAUCGCUAUCGCCCAUA--UUU-UUGGUAGUUGCCUGCCGACCACUUUC
(((...((((((.(((((((....)))))))))))))...-.))).---...........((((..(((((((..(((((((......--...-.)))))))))))))).))))...... ( -38.20)
>DroYak_CAF1 6089 101 - 1
AGCUGCUCUU------------UUUGGCAUCUGAAAAUUU-UGUUU---GUAUACAAACCGGUCACGCUGGCAUCGCUAUCGCCCAUA--UUU-UUGGUAGUUGCCUGCGGACCACUUUC
((.((((...------------...)))).))........-.((((---(....))))).((((.(((.((((..(((((((......--...-.))))))))))).)))))))...... ( -30.30)
>consensus
______________AUAUCAU_UUUGGAAUCUGAAGAUUU_UUUUC___GUAUACAAACCGGUCACGCUGGCAUCGCUAUCGCCCAUA__UUU_UUGGUAGUUGCCUGCGGACCACUUUC
............................................................((((.(((.((((..(((((((.............))))))))))).)))))))...... (-18.73 = -19.45 +   0.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:39 2006