Locus 5195

Sequence ID dm3.chr2R
Location 18,457,197 – 18,457,250
Length 53
Max. P 0.720677
window7126 window7127

overview

Window 6

Location 18,457,197 – 18,457,250
Length 53
Sequences 6
Columns 59
Reading direction forward
Mean pairwise identity 63.06
Shannon entropy 0.61355
G+C content 0.37941
Mean single sequence MFE -12.10
Consensus MFE -3.00
Energy contribution -3.53
Covariance contribution 0.53
Combinations/Pair 1.33
Mean z-score -2.32
Structure conservation index 0.25
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.42
SVM RNA-class probability 0.686522
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 18457197 53 + 21146708
-----AAACAACAUUUCUUAAUG-AGCACGUGUAGAGUGAAUCUACACCUGUUCUCUAC
-----.................(-((((.(((((((.....))))))).)))))..... ( -15.50, z-score =  -3.62, R)
>droPer1.super_2 7272516 52 + 9036312
AAAUCAGGUUGAACCGUGUAAAAUAACACAAACAGAAUGUA---ACAUCUGUUAC----
......((.....))((((......)))).((((((.....---...))))))..---- ( -10.00, z-score =  -1.69, R)
>dp4.chr3 7072950 52 + 19779522
AAAUCAGGUAGAACCGUGUAAAAUAACACAAACAGAAUGUA---ACAUCUGUUAC----
......((.....))((((......)))).((((((.....---...))))))..---- ( -10.00, z-score =  -2.15, R)
>droEre2.scaffold_4845 15097492 53 - 22589142
-----GAACAACAUCUCUUAAUG-AGCACGUGUAAAGUGAGUCUACACCUGUUCUCUGC
-----.................(-((((.(((((.........))))).)))))..... (  -9.60, z-score =  -0.43, R)
>droYak2.chr2R 15926391 53 + 21139217
-----AAACAACAUCUCUUAAUG-AGCACGUGUAAAGUGAGUCUACACCUGUUCUCUAC
-----.................(-((((.(((((.........))))).)))))..... (  -9.60, z-score =  -1.13, R)
>droSim1.chr2R 17047063 53 + 19596830
-----AAACAACAUCUCUUAAUG-AGCACGUGUAGAGUGAAUCUACACCUGCUCUCUAC
-----.................(-((((.(((((((.....))))))).)))))..... ( -17.90, z-score =  -4.89, R)
>consensus
_____AAACAACAUCUCUUAAUG_AGCACGUGUAGAGUGAAUCUACACCUGUUCUCUAC
........................((((.(((((.........))))).))))...... ( -3.00 =  -3.53 +   0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 18,457,197 – 18,457,250
Length 53
Sequences 6
Columns 59
Reading direction reverse
Mean pairwise identity 63.06
Shannon entropy 0.61355
G+C content 0.37941
Mean single sequence MFE -12.67
Consensus MFE -4.95
Energy contribution -5.28
Covariance contribution 0.34
Combinations/Pair 1.44
Mean z-score -1.51
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.50
SVM RNA-class probability 0.720677
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 18457197 53 - 21146708
GUAGAGAACAGGUGUAGAUUCACUCUACACGUGCU-CAUUAAGAAAUGUUGUUU-----
...(((..((.(((((((.....))))))).))))-).................----- ( -13.70, z-score =  -1.88, R)
>droPer1.super_2 7272516 52 - 9036312
----GUAACAGAUGU---UACAUUCUGUUUGUGUUAUUUUACACGGUUCAACCUGAUUU
----..((((((...---.....)))))).((((......))))((.....))...... (  -9.70, z-score =  -1.11, R)
>dp4.chr3 7072950 52 - 19779522
----GUAACAGAUGU---UACAUUCUGUUUGUGUUAUUUUACACGGUUCUACCUGAUUU
----..((((((...---.....)))))).((((......))))((.....))...... (  -9.70, z-score =  -1.35, R)
>droEre2.scaffold_4845 15097492 53 + 22589142
GCAGAGAACAGGUGUAGACUCACUUUACACGUGCU-CAUUAAGAGAUGUUGUUC-----
.....(((((((((((((.....)))))))...((-(.....)))...))))))----- ( -12.00, z-score =  -0.51, R)
>droYak2.chr2R 15926391 53 - 21139217
GUAGAGAACAGGUGUAGACUCACUUUACACGUGCU-CAUUAAGAGAUGUUGUUU-----
...(((..((.(((((((.....))))))).))))-).................----- ( -11.00, z-score =  -0.41, R)
>droSim1.chr2R 17047063 53 - 19596830
GUAGAGAGCAGGUGUAGAUUCACUCUACACGUGCU-CAUUAAGAGAUGUUGUUU-----
.....(((((.(((((((.....))))))).))))-).................----- ( -19.90, z-score =  -3.78, R)
>consensus
GUAGAGAACAGGUGUAGAUUCACUCUACACGUGCU_CAUUAAGAGAUGUUGUUU_____
........((.(((((((.....))))))).)).......................... ( -4.95 =  -5.28 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:43:38 2011