Locus 2419

Sequence ID	3R_DroMel_CAF1
Location	6,762,354 – 6,762,548
Length	194
Max. P	0.998881

overview

Window 6

Location	6,762,354 – 6,762,472
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.82
Mean single sequence MFE	-37.90
Consensus MFE	-31.91
Energy contribution	-32.11
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.75
Structure conservation index	0.84
SVM decision value	2.48
SVM RNA-class probability	0.994409
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6762354 118 - 27905053
GAGCUGGCCGAAAGGCCACGCCCAACACAACAUGACAACAUCAAUGUCAACAGGACAGCAG--CACACCGCCCCCAAAUGCCCUGUCCUCGCCGAAAUUCAUGGGACAACGUGGCCUGCA
......((....((((((((((((........(((((.......)))))..(((((((..(--((.............))).)))))))............))))....)))))))))). ( -35.42)
>DroSec_CAF1 26595 120 - 1
GAGCUGGCCGAAAGGCCACGCCCAACACAACAUGACAACAUCAAUGUCAACAGGACAGCAGGGCACACCGCCCCCAAAUGCCCUGUCCUCGCCGAAAUUCAUGGGGCAACGUGGCCUGCA
(.(((((((....))))).)).).........(((((.......)))))........(((((.(((...(((((...(((.....((......))....))))))))...))).))))). ( -44.00)
>DroSim_CAF1 30935 120 - 1
GAGCUGGCCGAAAGGCCACGCCCAACACAACAUGACAACAUCAAUGUCAACAGGACAGCAGCGCACACCGCCCCCAAAUGCCCUGUCCUCGCCGAAAUUCAUGGGGCAACGUGGCCUGCA
(.(((((((....))))).)).).........(((((.......)))))........((((.((.(((.(((((...(((.....((......))....))))))))...))))))))). ( -40.30)
>DroEre_CAF1 11043 118 - 1
GAGCUGGCCGAAAGGCCACGCCCAACGCAACAUGACAACAUCAAUGUCAACAGGACAGCAG--CACACCGCCCCCAAAUGCCCUGUCCUCUCCGAAAUUCAUGGGACAACGUGGCCUGCA
(.(((((((....))))).)).)...(((...(((((.......)))))..(((((((..(--((.............))).))))))).........(((((......)))))..))). ( -35.82)
>DroYak_CAF1 23202 118 - 1
GAGCUGGCCGAAAGGCCACGCCCAACACAACAUGACAACAUCAAUGUCAACAGGACAGCAG--CACACCGCCCCCAAAUGCCCUGUCCUCCACGAAAUUCAUGGCACAACGUGGCCUGCA
(.(((((((....))))).)).).........(((((.......)))))..(((((((..(--((.............))).)))))))(((((...............)))))...... ( -33.98)
>consensus
GAGCUGGCCGAAAGGCCACGCCCAACACAACAUGACAACAUCAAUGUCAACAGGACAGCAG__CACACCGCCCCCAAAUGCCCUGUCCUCGCCGAAAUUCAUGGGACAACGUGGCCUGCA
......((....((((((((((((........(((((.......)))))..(((((((((..................)))..))))))............))))....)))))))))). (-31.91 = -32.11 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	6,762,394 – 6,762,512
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.06
Mean single sequence MFE	-44.34
Consensus MFE	-39.36
Energy contribution	-39.96
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.00
Structure conservation index	0.89
SVM decision value	2.46
SVM RNA-class probability	0.994263
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6762394 118 + 27905053
CAUUUGGGGGCGGUGUG--CUGCUGUCCUGUUGACAUUGAUGUUGUCAUGUUGUGUUGGGCGUGGCCUUUCGGCCAGCUCGGCAAAUACCUGUUUAUGUUAUGCCUGGCACAUCAGAGCA
......((((((((...--..))))))))(((((((.......)))).((.(((((..(((((((((....))))(((..((((......))))...))))))))..))))).)).))). ( -43.90)
>DroSec_CAF1 26635 120 + 1
CAUUUGGGGGCGGUGUGCCCUGCUGUCCUGUUGACAUUGAUGUUGUCAUGUUGUGUUGGGCGUGGCCUUUCGGCCAGCUCGGCAAAUACCUGUUUAUGUUAUGCCUGCCACAUCAGGGCA
......(((((.....)))))...((((((.(((((.......)))))...((((..((((.(((((....)))))))))((((((((........)))).))))...)))).)))))). ( -44.90)
>DroSim_CAF1 30975 112 + 1
CAUUUGGGGGCGGUGUGCGCUGCUGUCCUGUUGACAUUGAUGUUGUCAUGUUGUGUUGGGCGUGGCCUUUCGGCCAGCUCGGCAAAUACCUGUUUAUGUUAUGCCUGGCACA--------
......((((((((.......))))))))..(((((.......)))))...(((((..(((((((((....))))(((..((((......))))...))))))))..)))))-------- ( -41.50)
>DroEre_CAF1 11083 118 + 1
CAUUUGGGGGCGGUGUG--CUGCUGUCCUGUUGACAUUGAUGUUGUCAUGUUGCGUUGGGCGUGGCCUUUCGGCCAGCUCGGCAAAUACCUGUUUAUGUUAUGCCUGGCACAUCAGGGCG
......((((((((...--..))))))))..(((((.......)))))....(((((((((.(((((....)))))))))))).....((((....(((((....)))))...)))))). ( -44.60)
>DroYak_CAF1 23242 118 + 1
CAUUUGGGGGCGGUGUG--CUGCUGUCCUGUUGACAUUGAUGUUGUCAUGUUGUGUUGGGCGUGGCCUUUCGGCCAGCUCGGCAAAUACCUGUUUAUGUUAUGCCUGGCACAUCAGGGCA
........(((((....--)))))((((((.(((((.......)))))...(((((..(((((((((....))))(((..((((......))))...))))))))..))))).)))))). ( -46.80)
>consensus
CAUUUGGGGGCGGUGUG__CUGCUGUCCUGUUGACAUUGAUGUUGUCAUGUUGUGUUGGGCGUGGCCUUUCGGCCAGCUCGGCAAAUACCUGUUUAUGUUAUGCCUGGCACAUCAGGGCA
......((((((((.......))))))))..(((((.......)))))((.((((..((((((((((....))))(((..((((......))))...)))))))))..)))).))..... (-39.36 = -39.96 +   0.60)

alignment

secondary structure

dotplot

Window 8

Location	6,762,394 – 6,762,512
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.06
Mean single sequence MFE	-35.86
Consensus MFE	-30.46
Energy contribution	-30.98
Covariance contribution	0.52
Combinations/Pair	1.07
Mean z-score	-2.94
Structure conservation index	0.85
SVM decision value	3.27
SVM RNA-class probability	0.998881
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6762394 118 - 27905053
UGCUCUGAUGUGCCAGGCAUAACAUAAACAGGUAUUUGCCGAGCUGGCCGAAAGGCCACGCCCAACACAACAUGACAACAUCAAUGUCAACAGGACAGCAG--CACACCGCCCCCAAAUG
(((((((.((((...((((..((........))...))))(.(((((((....))))).)).)..))))...(((((.......)))))......))).))--))............... ( -35.30)
>DroSec_CAF1 26635 120 - 1
UGCCCUGAUGUGGCAGGCAUAACAUAAACAGGUAUUUGCCGAGCUGGCCGAAAGGCCACGCCCAACACAACAUGACAACAUCAAUGUCAACAGGACAGCAGGGCACACCGCCCCCAAAUG
(((((((.((((...((((..((........))...))))(.(((((((....))))).)).)..))))...(((((.......))))).))))...)))((((.....))))....... ( -42.80)
>DroSim_CAF1 30975 112 - 1
--------UGUGCCAGGCAUAACAUAAACAGGUAUUUGCCGAGCUGGCCGAAAGGCCACGCCCAACACAACAUGACAACAUCAAUGUCAACAGGACAGCAGCGCACACCGCCCCCAAAUG
--------(((((...((....(((.....(((....)))(.(((((((....))))).)).)........)))..........((((.....))))))...)))))............. ( -31.10)
>DroEre_CAF1 11083 118 - 1
CGCCCUGAUGUGCCAGGCAUAACAUAAACAGGUAUUUGCCGAGCUGGCCGAAAGGCCACGCCCAACGCAACAUGACAACAUCAAUGUCAACAGGACAGCAG--CACACCGCCCCCAAAUG
.((((((((((((..((((..((........))...))))(.(((((((....))))).)).)...)).))))((((.......))))..))))...)).(--(.....))......... ( -34.80)
>DroYak_CAF1 23242 118 - 1
UGCCCUGAUGUGCCAGGCAUAACAUAAACAGGUAUUUGCCGAGCUGGCCGAAAGGCCACGCCCAACACAACAUGACAACAUCAAUGUCAACAGGACAGCAG--CACACCGCCCCCAAAUG
(((((((.((((...((((..((........))...))))(.(((((((....))))).)).)..))))...(((((.......))))).))))...)))(--(.....))......... ( -35.30)
>consensus
UGCCCUGAUGUGCCAGGCAUAACAUAAACAGGUAUUUGCCGAGCUGGCCGAAAGGCCACGCCCAACACAACAUGACAACAUCAAUGUCAACAGGACAGCAG__CACACCGCCCCCAAAUG
...((((.((((...((((..((........))...))))(.(((((((....))))).)).)..))))...(((((.......))))).)))).......................... (-30.46 = -30.98 +   0.52)

alignment

secondary structure

dotplot

Window 9

Location	6,762,432 – 6,762,548
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.24
Mean single sequence MFE	-36.19
Consensus MFE	-25.32
Energy contribution	-25.92
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.96
Structure conservation index	0.70
SVM decision value	0.42
SVM RNA-class probability	0.729218
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6762432 116 - 27905053
AUACUGGCCA----ACAACGGGGGAAUGGUGUAGGGAUGAUGCUCUGAUGUGCCAGGCAUAACAUAAACAGGUAUUUGCCGAGCUGGCCGAAAGGCCACGCCCAACACAACAUGACAACA
...(((....----....))).(..(((((((.(((.((..((((((.(((((...))))).))......(((....)))))))(((((....)))))))))).))))..)))..).... ( -38.00)
>DroSec_CAF1 26675 116 - 1
CUACUGGGCA----ACAACGGGGGAAUGGGGUAGGGAUGAUGCCCUGAUGUGGCAGGCAUAACAUAAACAGGUAUUUGCCGAGCUGGCCGAAAGGCCACGCCCAACACAACAUGACAACA
....(((((.----(((.(((((..((.(........).)).))))).)))(((.((((..((........))...))))..)))((((....))))..)))))................ ( -38.50)
>DroSim_CAF1 31015 105 - 1
AUACUGGGCA----ACAACGGGGGAAUGGGGUAGGGA-----------UGUGCCAGGCAUAACAUAAACAGGUAUUUGCCGAGCUGGCCGAAAGGCCACGCCCAACACAACAUGACAACA
......(...----.)...(..(..(((..((.(((.-----------(((((..((((..((........))...))))..)).((((....))))))))))...))..)))..)..). ( -33.40)
>DroEre_CAF1 11121 108 - 1
ACACUGGGCA----ACAACG--------UGGUAAGGAGGACGCCCUGAUGUGCCAGGCAUAACAUAAACAGGUAUUUGCCGAGCUGGCCGAAAGGCCACGCCCAACGCAACAUGACAACA
....(((((.----......--------(((((...(((....)))....)))))((((..((........))...))))..(.(((((....)))))))))))................ ( -34.90)
>DroYak_CAF1 23280 116 - 1
GCAGUGGACAGUGGACAGGG----UAAGGAGUAAGGAGGAUGCCCUGAUGUGCCAGGCAUAACAUAAACAGGUAUUUGCCGAGCUGGCCGAAAGGCCACGCCCAACACAACAUGACAACA
...((.....(((..(((((----((..............))))))).((((...((((..((........))...))))(.(((((((....))))).)).)..)))).)))....)). ( -36.14)
>consensus
AUACUGGGCA____ACAACGGGGGAAUGGGGUAGGGAGGAUGCCCUGAUGUGCCAGGCAUAACAUAAACAGGUAUUUGCCGAGCUGGCCGAAAGGCCACGCCCAACACAACAUGACAACA
....(((((..........................................((..((((..((........))...))))..))(((((....))))).)))))................ (-25.32 = -25.92 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:26 2006