Locus 1241

Sequence ID	3L_DroMel_CAF1
Location	3,532,085 – 3,532,213
Length	128
Max. P	0.938049

overview

Window 3

Location	3,532,085 – 3,532,191
Length	106
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	96.24
Mean single sequence MFE	-32.44
Consensus MFE	-27.68
Energy contribution	-28.16
Covariance contribution	0.48
Combinations/Pair	1.07
Mean z-score	-1.37
Structure conservation index	0.85
SVM decision value	0.11
SVM RNA-class probability	0.588484
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3532085 106 + 23771897
UUUGCCUGGUGAAUAAAUGAUGCGUGUUUUAUGGCGACGCUGAUGGAUGUGGCUGCCAAAGGCGUAGAAAGCUUGGCCAGCAAGGGUUAAUGGCAGCCAGA-ACUAG
.....(((((...........(((((((....))).)))).......(.(((((((((.((((.......))))((((......))))..))))))))).)-))))) ( -33.70)
>DroSec_CAF1 62297 106 + 1
UUUGUGUGGUGAAUAAAUGAUGCGUGUUUUAUGGCGACGCUGAUGGAUGUGGCUGCCAAAGGCGUAGAAAGCUUGGCCAGCAAGGCUUAAUGGCAGCCAGA-ACUAA
...((((.((..(((((..........))))).)).))))...(((.(.(((((((((.((((.......))))((((.....))))...))))))))).)-.))). ( -35.50)
>DroSim_CAF1 63334 106 + 1
UUUGCCUGGUGAAUAAAUGAUGCGUGUUUUAUGGCGACGCUGAUGGAUGUGGCUGCCAAAGGCGUAGAAAGCUUGGCCAGCAAGGGUUAAUGGCAGCCAGA-ACUAA
.(((((..(((((...(((...)))..))))))))))......(((.(.(((((((((.((((.......))))((((......))))..))))))))).)-.))). ( -32.50)
>DroEre_CAF1 80118 107 + 1
UUUGCCUGGUGAAUAAAUGAUGCGUGUUUUAUAGCGACGCUGAUGGAUGGGGCUGCCAAAGGCGUAGAAAGCUUGGCCAGCAAGGGUUAAUGGCACCCAGAUAUUAG
.....................(((((((....))).))))(((((..((((..(((((.((((.......))))((((......))))..)))))))))..))))). ( -28.20)
>DroYak_CAF1 65052 106 + 1
UUUGCCUGGUGAAUAAAUGAUGCGUGUUUUAUGGCGACGCUGAUGGAUGGGGCUGCCAAAGGCGUAGAAAGCUUGGCCAGCAAGGGUUAAUGGCAGCCAGA-ACUAG
.....(((((...........(((((((....))).))))..........((((((((.((((.......))))((((......))))..))))))))...-))))) ( -32.30)
>consensus
UUUGCCUGGUGAAUAAAUGAUGCGUGUUUUAUGGCGACGCUGAUGGAUGUGGCUGCCAAAGGCGUAGAAAGCUUGGCCAGCAAGGGUUAAUGGCAGCCAGA_ACUAG
.....(((((...........(((((((....))).))))..........((((((((.((((.......))))((((......))))..))))))))....))))) (-27.68 = -28.16 +   0.48)

alignment

secondary structure

dotplot

Window 4

Location	3,532,085 – 3,532,191
Length	106
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	96.24
Mean single sequence MFE	-22.78
Consensus MFE	-20.64
Energy contribution	-20.84
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.54
Structure conservation index	0.91
SVM decision value	1.27
SVM RNA-class probability	0.938049
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3532085 106 - 23771897
CUAGU-UCUGGCUGCCAUUAACCCUUGCUGGCCAAGCUUUCUACGCCUUUGGCAGCCACAUCCAUCAGCGUCGCCAUAAAACACGCAUCAUUUAUUCACCAGGCAAA
...((-(.(((((((((.........(((.....)))............))))))))).........((((.(........)))))...............)))... ( -23.00)
>DroSec_CAF1 62297 106 - 1
UUAGU-UCUGGCUGCCAUUAAGCCUUGCUGGCCAAGCUUUCUACGCCUUUGGCAGCCACAUCCAUCAGCGUCGCCAUAAAACACGCAUCAUUUAUUCACCACACAAA
.....-..(((((((((....(((.....)))...((.......))...))))))))).........((((.(........)))))..................... ( -25.30)
>DroSim_CAF1 63334 106 - 1
UUAGU-UCUGGCUGCCAUUAACCCUUGCUGGCCAAGCUUUCUACGCCUUUGGCAGCCACAUCCAUCAGCGUCGCCAUAAAACACGCAUCAUUUAUUCACCAGGCAAA
...((-(.(((((((((.........(((.....)))............))))))))).........((((.(........)))))...............)))... ( -23.00)
>DroEre_CAF1 80118 107 - 1
CUAAUAUCUGGGUGCCAUUAACCCUUGCUGGCCAAGCUUUCUACGCCUUUGGCAGCCCCAUCCAUCAGCGUCGCUAUAAAACACGCAUCAUUUAUUCACCAGGCAAA
.........((((.......))))(((((.(((((((.......))..)))))..............((((.(........)))))...............))))). ( -21.00)
>DroYak_CAF1 65052 106 - 1
CUAGU-UCUGGCUGCCAUUAACCCUUGCUGGCCAAGCUUUCUACGCCUUUGGCAGCCCCAUCCAUCAGCGUCGCCAUAAAACACGCAUCAUUUAUUCACCAGGCAAA
...((-(..((((((((.........(((.....)))............))))))))..........((((.(........)))))...............)))... ( -21.60)
>consensus
CUAGU_UCUGGCUGCCAUUAACCCUUGCUGGCCAAGCUUUCUACGCCUUUGGCAGCCACAUCCAUCAGCGUCGCCAUAAAACACGCAUCAUUUAUUCACCAGGCAAA
.........((((((((.........(((.....)))............))))))))..........((((.(........)))))..................... (-20.64 = -20.84 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	3,532,115 – 3,532,213
Length	98
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	91.76
Mean single sequence MFE	-32.40
Consensus MFE	-23.36
Energy contribution	-23.44
Covariance contribution	0.08
Combinations/Pair	1.08
Mean z-score	-2.46
Structure conservation index	0.72
SVM decision value	0.54
SVM RNA-class probability	0.776199
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3532115 98 + 23771897
AUGGCGACGCUGAUGGAUGUGGCUGCCAAAGGCGUAGAAAGCUUGGCCAGCAAGGGUUAAUGGCAGCCAGA-ACUAGA---------AAUUUAUGUUUGCGUGAAGUU
......((((...(((.(.(((((((((.((((.......))))((((......))))..))))))))).)-.))).(---------(((....))))))))...... ( -30.60)
>DroSec_CAF1 62327 98 + 1
AUGGCGACGCUGAUGGAUGUGGCUGCCAAAGGCGUAGAAAGCUUGGCCAGCAAGGCUUAAUGGCAGCCAGA-ACUAAA---------AAUUUAUGUUUGCGUGAAGUU
......((((...(((.(.(((((((((.((((.......))))((((.....))))...))))))))).)-.))).(---------(((....))))))))...... ( -32.30)
>DroSim_CAF1 63364 98 + 1
AUGGCGACGCUGAUGGAUGUGGCUGCCAAAGGCGUAGAAAGCUUGGCCAGCAAGGGUUAAUGGCAGCCAGA-ACUAAA---------AAUUUAUGUUUGCGUGAAGUU
......((((...(((.(.(((((((((.((((.......))))((((......))))..))))))))).)-.))).(---------(((....))))))))...... ( -30.50)
>DroEre_CAF1 80148 108 + 1
AUAGCGACGCUGAUGGAUGGGGCUGCCAAAGGCGUAGAAAGCUUGGCCAGCAAGGGUUAAUGGCACCCAGAUAUUAGAAAUAGUCGGAAUUUAUGUUUGCGUGAAAUU
....((((.((((((..((((..(((((.((((.......))))((((......))))..)))))))))..)))))).....))))...((((((....))))))... ( -34.00)
>DroYak_CAF1 65082 98 + 1
AUGGCGACGCUGAUGGAUGGGGCUGCCAAAGGCGUAGAAAGCUUGGCCAGCAAGGGUUAAUGGCAGCCAGA-ACUAGA---------CAUUUGUGUUUACGUGAAGUU
(((..(((((.((((..(((((((((((.((((.......))))((((......))))..))))))))...-.)))..---------)))).)))))..)))...... ( -34.60)
>consensus
AUGGCGACGCUGAUGGAUGUGGCUGCCAAAGGCGUAGAAAGCUUGGCCAGCAAGGGUUAAUGGCAGCCAGA_ACUAGA_________AAUUUAUGUUUGCGUGAAGUU
.((((...))))........((((((((.((((.......))))((((......))))..)))))))).....................((((((....))))))... (-23.36 = -23.44 +   0.08)

alignment

secondary structure

dotplot

Window 6

Location	3,532,115 – 3,532,213
Length	98
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	91.76
Mean single sequence MFE	-22.16
Consensus MFE	-17.92
Energy contribution	-18.16
Covariance contribution	0.24
Combinations/Pair	1.06
Mean z-score	-1.90
Structure conservation index	0.81
SVM decision value	1.18
SVM RNA-class probability	0.927478
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3532115 98 - 23771897
AACUUCACGCAAACAUAAAUU---------UCUAGU-UCUGGCUGCCAUUAACCCUUGCUGGCCAAGCUUUCUACGCCUUUGGCAGCCACAUCCAUCAGCGUCGCCAU
......((((.(((.......---------....))-).(((((((((.........(((.....)))............))))))))).........))))...... ( -22.20)
>DroSec_CAF1 62327 98 - 1
AACUUCACGCAAACAUAAAUU---------UUUAGU-UCUGGCUGCCAUUAAGCCUUGCUGGCCAAGCUUUCUACGCCUUUGGCAGCCACAUCCAUCAGCGUCGCCAU
......((((.(((.(((...---------.)))))-).(((((((((....(((.....)))...((.......))...))))))))).........))))...... ( -25.00)
>DroSim_CAF1 63364 98 - 1
AACUUCACGCAAACAUAAAUU---------UUUAGU-UCUGGCUGCCAUUAACCCUUGCUGGCCAAGCUUUCUACGCCUUUGGCAGCCACAUCCAUCAGCGUCGCCAU
......((((.(((.(((...---------.)))))-).(((((((((.........(((.....)))............))))))))).........))))...... ( -22.50)
>DroEre_CAF1 80148 108 - 1
AAUUUCACGCAAACAUAAAUUCCGACUAUUUCUAAUAUCUGGGUGCCAUUAACCCUUGCUGGCCAAGCUUUCUACGCCUUUGGCAGCCCCAUCCAUCAGCGUCGCUAU
......((((..............................((((.......))))..((((.((((((.......))..))))))))...........))))...... ( -20.60)
>DroYak_CAF1 65082 98 - 1
AACUUCACGUAAACACAAAUG---------UCUAGU-UCUGGCUGCCAUUAACCCUUGCUGGCCAAGCUUUCUACGCCUUUGGCAGCCCCAUCCAUCAGCGUCGCCAU
((((..((((........)))---------)..)))-)..((((((((.........(((.....)))............)))))))).................... ( -20.50)
>consensus
AACUUCACGCAAACAUAAAUU_________UCUAGU_UCUGGCUGCCAUUAACCCUUGCUGGCCAAGCUUUCUACGCCUUUGGCAGCCACAUCCAUCAGCGUCGCCAU
......((((.......................((...))((((((((.........(((.....)))............))))))))..........))))...... (-17.92 = -18.16 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:53 2006