Locus 6920

Sequence ID	3L_DroMel_CAF1
Location	18,670,488 – 18,670,641
Length	153
Max. P	0.627397

overview

Window 7

Location	18,670,488 – 18,670,602
Length	114
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.00
Mean single sequence MFE	-28.91
Consensus MFE	-19.58
Energy contribution	-19.97
Covariance contribution	0.39
Combinations/Pair	1.11
Mean z-score	-1.66
Structure conservation index	0.68
SVM decision value	-0.02
SVM RNA-class probability	0.521888
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18670488 114 + 23771897
ACUUUCUCCCCUUUUAUAGGACUUUUUU--UUUCCC-CCUUGUCCAGGCAGCCGCUUAAUGCAAUCAAAAUGCCUCUGGCUGAGUGCCGGAAUGGCAAUUACUACAGCCACAGUU---AC
..................((((......--......-....)))).(((....((.....))........((((((((((.....))))))..)))).........)))......---.. ( -27.59)
>DroSec_CAF1 7754 113 + 1
ACUUUCUCCCCUUUCACAGGACAUUUUU---UUUUG-CCCUAUCCAGGCAGCCGCUUAAUGCAAUCAAAAUGCCGCUGGCCGAGUGCCGGAAUGGCAAUUACUACAGCCACAGUU---AC
.................(((.((.....---...))-.))).....(((....((.....))........((((.(((((.....)))))...)))).........)))......---.. ( -24.00)
>DroAna_CAF1 7344 110 + 1
AUU-----CCCUUUUGCGUGGCAGAUUU---UUUUGCUUUUAUCCAGGCACCCGCUUAAUGCAAUCAAAAUGCCACUGGUCGAGUGCCGGAAUGGCAAUUGCCGUUGCAAAAGGCA--GC
...-----.(((((((((.((((((...---.))))))....(((.(((((.((((....(((.......)))....)).)).))))))))(((((....))))))))))))))..--.. ( -38.70)
>DroSim_CAF1 7695 116 + 1
ACUUUCUCCCCUUUCACAGGACAUUUUUUUUUUUUG-CGUUAUCCAGGCAGCCGCUUAAUGCAAUCAAAAUGCCUCUGGCCGACUGCCGGAAUGGCAAUUACUACAGCCACAGUA---AC
.........(((.....))).......((((..(((-(((((....(((....)))))))))))..))))((((((((((.....))))))..)))).(((((........))))---). ( -26.20)
>DroEre_CAF1 7666 109 + 1
ACUUUCUCCCCU-UUGCAGGACAUUUUU------UG-CCUUAUCCAGGCAGCCGCCUAAUGCAAUCAAAAUGCCUCUGGCCGAGUGCCGGAAUGGCAAUUACUACUGCCACAGUU---GC
............-..((((........(------((-((...(((.((((.(.(((....(((.......)))....))).)..)))))))..)))))......)))).......---.. ( -29.14)
>DroYak_CAF1 7813 113 + 1
ACUUUCUCCCCUUUUGCAGGACAUUUUU------UC-CUUUAUCCUGGCAGCCGCUUAAUGCAAUCAAAAUGCCUCUGGCCGAGUGCCGGAAUGGCAAUUACUACUGCCACAGUUACUGC
...............((((((.......------))-).......((((((..((.....))........((((((((((.....))))))..)))).......)))))).......))) ( -27.80)
>consensus
ACUUUCUCCCCUUUUACAGGACAUUUUU___UUUUG_CCUUAUCCAGGCAGCCGCUUAAUGCAAUCAAAAUGCCUCUGGCCGAGUGCCGGAAUGGCAAUUACUACAGCCACAGUU___AC
.........(((.....)))..........................(((....((.....))........((((((((((.....))))))..)))).........)))........... (-19.58 = -19.97 +   0.39)

alignment

secondary structure

dotplot

Window 8

Location	18,670,525 – 18,670,641
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.60
Mean single sequence MFE	-33.07
Consensus MFE	-22.15
Energy contribution	-22.75
Covariance contribution	0.60
Combinations/Pair	1.08
Mean z-score	-1.89
Structure conservation index	0.67
SVM decision value	0.19
SVM RNA-class probability	0.627397
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18670525 116 + 23771897
UGUCCAGGCAGCCGCUUAAUGCAAUCAAAAUGCCUCUGGCUGAGUGCCGGAAUGGCAAUUACUACAGCCACAGUU---ACUG-CACGUCUGCUACCUAUGGCACAGAAUAAAGCCAUUUA
......(((....((.....))..((....((((((((((.....))))))..)))).........((((.((..---...(-((....)))...)).))))...)).....)))..... ( -31.70)
>DroSec_CAF1 7790 116 + 1
UAUCCAGGCAGCCGCUUAAUGCAAUCAAAAUGCCGCUGGCCGAGUGCCGGAAUGGCAAUUACUACAGCCACAGUU---ACUG-CACGUCUGCUACCUAUGGCACUGAAUAAAGCCAUUUA
......(((....((.....))..(((...((((.(((((.....)))))...)))).........((((.((..---...(-((....)))...)).))))..))).....)))..... ( -30.40)
>DroAna_CAF1 7376 93 + 1
UAUCCAGGCACCCGCUUAAUGCAAUCAAAAUGCCACUGGUCGAGUGCCGGAAUGGCAAUUGCCGUUGCAAAAGGCA--GCUGGAACAGCUGCUAC-------------------------
......(((((.((((....(((.......)))....)).)).)))))(.((((((....)))))).)....((((--((((...))))))))..------------------------- ( -36.00)
>DroSim_CAF1 7734 116 + 1
UAUCCAGGCAGCCGCUUAAUGCAAUCAAAAUGCCUCUGGCCGACUGCCGGAAUGGCAAUUACUACAGCCACAGUA---ACUG-CACGUCUGCUACCUAUGGCACUGAAUAAAGCCAUUUA
..(((.((((((.(((....(((.......)))....))).).))))))))(((((..........((((.((..---...(-((....)))...)).))))..........)))))... ( -31.35)
>DroEre_CAF1 7698 116 + 1
UAUCCAGGCAGCCGCCUAAUGCAAUCAAAAUGCCUCUGGCCGAGUGCCGGAAUGGCAAUUACUACUGCCACAGUU---GCUG-CACUUCUGUUAGCCAUGGCCCAGAAGAAAGCCAUUUA
......(((((..((.....))........((((((((((.....))))))..)))).......)))))......---(((.-..((((((...((....)).))))))..)))...... ( -35.60)
>DroYak_CAF1 7846 119 + 1
UAUCCUGGCAGCCGCUUAAUGCAAUCAAAAUGCCUCUGGCCGAGUGCCGGAAUGGCAAUUACUACUGCCACAGUUACUGCUG-CACUUCUGCUACCUAUGGCACAGCAUAAAGCCAUUUA
.....((((((..((.....))........((((((((((.....))))))..)))).......))))))..(((..(((((-......(((((....))))))))))...)))...... ( -33.40)
>consensus
UAUCCAGGCAGCCGCUUAAUGCAAUCAAAAUGCCUCUGGCCGAGUGCCGGAAUGGCAAUUACUACAGCCACAGUU___ACUG_CACGUCUGCUACCUAUGGCACAGAAUAAAGCCAUUUA
......(((((..((.....))........((((((((((.....))))))..)))).............(((......)))......)))))....(((((..........)))))... (-22.15 = -22.75 +   0.60)

alignment

secondary structure

dotplot

Window 9

Location	18,670,525 – 18,670,641
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.60
Mean single sequence MFE	-40.49
Consensus MFE	-22.71
Energy contribution	-24.77
Covariance contribution	2.06
Combinations/Pair	1.07
Mean z-score	-2.41
Structure conservation index	0.56
SVM decision value	0.04
SVM RNA-class probability	0.553701
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18670525 116 - 23771897
UAAAUGGCUUUAUUCUGUGCCAUAGGUAGCAGACGUG-CAGU---AACUGUGGCUGUAGUAAUUGCCAUUCCGGCACUCAGCCAGAGGCAUUUUGAUUGCAUUAAGCGGCUGCCUGGACA
...(((((..........)))))(((((((.(..(((-((((---..((.((((((.(((....(((.....)))))))))))).))........)))))))....).)))))))..... ( -41.60)
>DroSec_CAF1 7790 116 - 1
UAAAUGGCUUUAUUCAGUGCCAUAGGUAGCAGACGUG-CAGU---AACUGUGGCUGUAGUAAUUGCCAUUCCGGCACUCGGCCAGCGGCAUUUUGAUUGCAUUAAGCGGCUGCCUGGAUA
...(((((..........)))))(((((((.(..(((-((((---..(((((((((.(((....(((.....)))))))))))).))).......)))))))....).)))))))..... ( -39.80)
>DroAna_CAF1 7376 93 - 1
-------------------------GUAGCAGCUGUUCCAGC--UGCCUUUUGCAACGGCAAUUGCCAUUCCGGCACUCGACCAGUGGCAUUUUGAUUGCAUUAAGCGGGUGCCUGGAUA
-------------------------((((((((((...))))--)))....)))...(((....)))..(((((((((((.......(((.......)))......)))))))).))).. ( -36.72)
>DroSim_CAF1 7734 116 - 1
UAAAUGGCUUUAUUCAGUGCCAUAGGUAGCAGACGUG-CAGU---UACUGUGGCUGUAGUAAUUGCCAUUCCGGCAGUCGGCCAGAGGCAUUUUGAUUGCAUUAAGCGGCUGCCUGGAUA
...(((((..........)))))(((((((.(..(((-((((---((((.((((((.....((((((.....)))))))))))).))......)))))))))....).)))))))..... ( -43.10)
>DroEre_CAF1 7698 116 - 1
UAAAUGGCUUUCUUCUGGGCCAUGGCUAACAGAAGUG-CAGC---AACUGUGGCAGUAGUAAUUGCCAUUCCGGCACUCGGCCAGAGGCAUUUUGAUUGCAUUAGGCGGCUGCCUGGAUA
......(((..(((((((((....)))..))))))..-.)))---....((((((((....))))))))(((((((..((.((.((.(((.......))).)).))))..)))).))).. ( -41.40)
>DroYak_CAF1 7846 119 - 1
UAAAUGGCUUUAUGCUGUGCCAUAGGUAGCAGAAGUG-CAGCAGUAACUGUGGCAGUAGUAAUUGCCAUUCCGGCACUCGGCCAGAGGCAUUUUGAUUGCAUUAAGCGGCUGCCAGGAUA
...(((((..........))))).((((((.((((((-(....((....((((((((....))))))))....)).(((.....))))))))))...(((.....)))))))))...... ( -40.30)
>consensus
UAAAUGGCUUUAUUCUGUGCCAUAGGUAGCAGACGUG_CAGC___AACUGUGGCAGUAGUAAUUGCCAUUCCGGCACUCGGCCAGAGGCAUUUUGAUUGCAUUAAGCGGCUGCCUGGAUA
...(((((..........(((((((...((..........)).....)))))))..........)))))(((((((.(((.......(((.......)))......))).)))).))).. (-22.71 = -24.77 +   2.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:04 2006