Locus 3089

Sequence ID	3R_DroMel_CAF1
Location	8,148,251 – 8,148,432
Length	181
Max. P	0.982925

overview

Window 2

Location	8,148,251 – 8,148,363
Length	112
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	75.66
Mean single sequence MFE	-31.03
Consensus MFE	-25.95
Energy contribution	-26.12
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-2.22
Structure conservation index	0.84
SVM decision value	1.93
SVM RNA-class probability	0.982925
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8148251 112 + 27905053
GAAACAGAUGCAAAAAGUUGAAUCUCAAUUCG-----UUGCCUCCUGUGAGGAUUGAACUCACGACCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAAGAGGCUCACAUG
(((..((((.(((....))).))))...)))(-----(.(((((.((((((.......))))))....((((((.....)))))).((((.......))))....)))))..))... ( -31.60)
>DroPse_CAF1 72255 97 + 1
-AAAUAUA----------UGAAA----CUUCU-----AUGCCUCCUGUGAGAAUUGAACUCACGGCCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAGGAGGCUUGCUUG
-.......----------.....----.....-----..((((((((((((.......))))).....((((((.....)))))).((((.......))))..)))))))....... ( -31.10)
>DroWil_CAF1 70034 113 + 1
AAAAAAGGAGAAUGAAA--GCAUCCCCCUUUGAACAUUUGCCUCCUGUGAGAAUUGAACUCACGACCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAGAAGGCAU--CUG
...(((((.(.(((...--.))).).)))))...((..(((((.(((((((.......))))).....((((((.....)))))).((((.......))))..)).))))).--.)) ( -31.60)
>DroMoj_CAF1 107165 108 + 1
UAUUAAC-C--AAAAAUAUCGAU-UCAGUUCG-----UUGCCUCCUGUGAGAAUUGAACUCACGGCCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAAGAGGCACAUAUC
.......-.--........(((.-.....)))-----.(((((((((((((.......)))))))...((((((.....)))))).((((.......))))....))))))...... ( -31.00)
>DroAna_CAF1 38669 105 + 1
GAGUCA-AUAAAAAAAG--GAAACAC-UC--------UUGCCUCCUGUGAGGAUUGAACUCACGACCCCUGGUUUACAAGACCAGUGCUCUACCACUGAGCUAAAGAGGCCUUCCUG
......-........((--(((...(-((--------((......((((((.......))))))....((((((.....)))))).((((.......))))..)))))...))))). ( -29.80)
>DroPer_CAF1 73791 97 + 1
-AAAUAUA----------UGAAA----CUUCU-----AUGCCUCCUGUGAGAAUUGAACUCACGGCCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAGGAGGCUUGCUUG
-.......----------.....----.....-----..((((((((((((.......))))).....((((((.....)))))).((((.......))))..)))))))....... ( -31.10)
>consensus
_AAAAAGA___AAAAA__UGAAA__C_CUUCG_____UUGCCUCCUGUGAGAAUUGAACUCACGACCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAAGAGGCUUACAUG
.......................................(((((.((((((.......))))))....((((((.....)))))).((((.......))))....)))))....... (-25.95 = -26.12 +   0.17)

alignment

secondary structure

dotplot

Window 3

Location	8,148,251 – 8,148,363
Length	112
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	75.66
Mean single sequence MFE	-34.02
Consensus MFE	-29.29
Energy contribution	-28.90
Covariance contribution	-0.39
Combinations/Pair	1.10
Mean z-score	-2.02
Structure conservation index	0.86
SVM decision value	1.82
SVM RNA-class probability	0.978653
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8148251 112 - 27905053
CAUGUGAGCCUCUUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGUCGUGAGUUCAAUCCUCACAGGAGGCAA-----CGAAUUGAGAUUCAACUUUUUGCAUCUGUUUC
(((.(((((.......))))))))(((((((((((((.......)))))(((((.(.(((((..(((.....)))(....-----)))))).)))))).......))).)))))... ( -33.50)
>DroPse_CAF1 72255 97 - 1
CAAGCAAGCCUCCUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGCCGUGAGUUCAAUUCUCACAGGAGGCAU-----AGAAG----UUUCA----------UAUAUUU-
.......(((((((..((((.......))))...((((((........))))))(((((.......))))))))))))..-----.....----.....----------.......- ( -32.00)
>DroWil_CAF1 70034 113 - 1
CAG--AUGCCUUCUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGUCGUGAGUUCAAUUCUCACAGGAGGCAAAUGUUCAAAGGGGGAUGC--UUUCAUUCUCCUUUUUU
((.--.((((((((..((((.......)))).(((((.......))))).....(((((.......)))))))))))))..))...(((((((((((.--...)))))))))))... ( -41.10)
>DroMoj_CAF1 107165 108 - 1
GAUAUGUGCCUCUUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGCCGUGAGUUCAAUUCUCACAGGAGGCAA-----CGAACUGA-AUCGAUAUUUUU--G-GUUAAUA
......((((((((..((((.......))))...((((((........))))))(((((.......))))))))))))).-----..(((..(-(........)).--.-))).... ( -33.60)
>DroAna_CAF1 38669 105 - 1
CAGGAAGGCCUCUUUAGCUCAGUGGUAGAGCACUGGUCUUGUAAACCAGGGGUCGUGAGUUCAAUCCUCACAGGAGGCAA--------GA-GUGUUUC--CUUUUUUUAU-UGACUC
......(((((.....((((.......)))).(((((.......))))))))))(((((.......)))))((((((((.--------..-.))))))--))........-...... ( -31.90)
>DroPer_CAF1 73791 97 - 1
CAAGCAAGCCUCCUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGCCGUGAGUUCAAUUCUCACAGGAGGCAU-----AGAAG----UUUCA----------UAUAUUU-
.......(((((((..((((.......))))...((((((........))))))(((((.......))))))))))))..-----.....----.....----------.......- ( -32.00)
>consensus
CAAGCAAGCCUCCUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGCCGUGAGUUCAAUUCUCACAGGAGGCAA_____CGAAG_G__AUUCA__UUUUU___UAUAUUU_
.......(((((((..((((.......)))).(((((.......))))).....(((((.......))))))))))))....................................... (-29.29 = -28.90 +  -0.39)

alignment

secondary structure

dotplot

Window 4

Location	8,148,283 – 8,148,392
Length	109
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	76.91
Mean single sequence MFE	-31.62
Consensus MFE	-25.95
Energy contribution	-26.12
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-2.28
Structure conservation index	0.82
SVM decision value	1.81
SVM RNA-class probability	0.978357
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8148283 109 + 27905053
UUGCCUCCUGUGAGGAUUGAACUCACGACCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAAGAGGCUCACAUGAAC-GUCUUG-AAAA-AUAACUAAAAUAUUAG
..(((((.((((((.......))))))....((((((.....)))))).((((.......))))....)))))..........-......-....-................ ( -27.60)
>DroPse_CAF1 72272 110 + 1
AUGCCUCCUGUGAGAAUUGAACUCACGGCCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAGGAGGCUUGCUUGAAA-AGAACGCACCA-UCAAGCAAUAUAAAAG
..((((((((((((.......))))).....((((((.....)))))).((((.......))))..)))))))((((((((..-...........-))))))))........ ( -38.72)
>DroWil_CAF1 70069 96 + 1
UUGCCUCCUGUGAGAAUUGAACUCACGACCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAGAAGGCAU--CUGACA--UAUUG-AAAG-AAAAGU----------
.(((((.(((((((.......))))).....((((((.....)))))).((((.......))))..)).)))))(--((..(.--....)-..))-).....---------- ( -25.70)
>DroMoj_CAF1 107193 108 + 1
UUGCCUCCUGUGAGAAUUGAACUCACGGCCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAAGAGGCACAUAUCGAUCAUAUAG-AGAACAGAAGU---UGAAGAA
.(((((((((((((.......)))))))...((((((.....)))))).((((.......))))....))))))....(((((.......-.........))---))).... ( -30.09)
>DroAna_CAF1 38694 97 + 1
UUGCCUCCUGUGAGGAUUGAACUCACGACCCCUGGUUUACAAGACCAGUGCUCUACCACUGAGCUAAAGAGGCCUUCCUGGAG---------------AAGUGAAAUUUUUG
..(((((.((((((.......))))))....((((((.....)))))).((((.......))))....)))))((((.....)---------------)))........... ( -28.90)
>DroPer_CAF1 73808 110 + 1
AUGCCUCCUGUGAGAAUUGAACUCACGGCCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAGGAGGCUUGCUUGAAA-AGAACGCACCA-UCAAGCAAUAUAAAAG
..((((((((((((.......))))).....((((((.....)))))).((((.......))))..)))))))((((((((..-...........-))))))))........ ( -38.72)
>consensus
UUGCCUCCUGUGAGAAUUGAACUCACGACCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAAGAGGCUUACAUGAAA_AUAUCG_AAAA_ACAAGUAA_AUAAAAG
..(((((.((((((.......))))))....((((((.....)))))).((((.......))))....)))))....................................... (-25.95 = -26.12 +   0.17)

alignment

secondary structure

dotplot

Window 5

Location	8,148,283 – 8,148,392
Length	109
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	76.91
Mean single sequence MFE	-33.68
Consensus MFE	-29.29
Energy contribution	-28.90
Covariance contribution	-0.39
Combinations/Pair	1.10
Mean z-score	-2.10
Structure conservation index	0.87
SVM decision value	1.69
SVM RNA-class probability	0.972280
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8148283 109 - 27905053
CUAAUAUUUUAGUUAU-UUUU-CAAGAC-GUUCAUGUGAGCCUCUUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGUCGUGAGUUCAAUCCUCACAGGAGGCAA
((((....))))....-....-......-..........(((((((..((((.......)))).(((((.......))))).....(((((.......)))))))))))).. ( -28.20)
>DroPse_CAF1 72272 110 - 1
CUUUUAUAUUGCUUGA-UGGUGCGUUCU-UUUCAAGCAAGCCUCCUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGCCGUGAGUUCAAUUCUCACAGGAGGCAU
........((((((((-.((......))-..))))))))(((((((..((((.......))))...((((((........))))))(((((.......)))))))))))).. ( -42.00)
>DroWil_CAF1 70069 96 - 1
----------ACUUUU-CUUU-CAAUA--UGUCAG--AUGCCUUCUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGUCGUGAGUUCAAUUCUCACAGGAGGCAA
----------......-....-.....--......--.((((((((..((((.......)))).(((((.......))))).....(((((.......))))))))))))). ( -28.90)
>DroMoj_CAF1 107193 108 - 1
UUCUUCA---ACUUCUGUUCU-CUAUAUGAUCGAUAUGUGCCUCUUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGCCGUGAGUUCAAUUCUCACAGGAGGCAA
.......---...........-................((((((((..((((.......))))...((((((........))))))(((((.......))))))))))))). ( -30.00)
>DroAna_CAF1 38694 97 - 1
CAAAAAUUUCACUU---------------CUCCAGGAAGGCCUCUUUAGCUCAGUGGUAGAGCACUGGUCUUGUAAACCAGGGGUCGUGAGUUCAAUCCUCACAGGAGGCAA
...........(((---------------(.....))))(((((((..((((.......)))).(((((.......))))).....(((((.......)))))))))))).. ( -31.00)
>DroPer_CAF1 73808 110 - 1
CUUUUAUAUUGCUUGA-UGGUGCGUUCU-UUUCAAGCAAGCCUCCUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGCCGUGAGUUCAAUUCUCACAGGAGGCAU
........((((((((-.((......))-..))))))))(((((((..((((.......))))...((((((........))))))(((((.......)))))))))))).. ( -42.00)
>consensus
CUAUUAU_UUACUUGU_UUGU_CAAUAU_UUUCAAGCAAGCCUCCUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGCCGUGAGUUCAAUUCUCACAGGAGGCAA
.......................................(((((((..((((.......)))).(((((.......))))).....(((((.......)))))))))))).. (-29.29 = -28.90 +  -0.39)

alignment

secondary structure

dotplot

Window 6

Location	8,148,323 – 8,148,432
Length	109
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	81.10
Mean single sequence MFE	-30.94
Consensus MFE	-13.73
Energy contribution	-14.62
Covariance contribution	0.89
Combinations/Pair	1.10
Mean z-score	-3.04
Structure conservation index	0.44
SVM decision value	0.55
SVM RNA-class probability	0.778319
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8148323 109 + 27905053
AAGACCAGUGCUCUGCCACUGAGCUAAAGAGGCUCACAUGAACGUCUUG-AAAAAUAACUAAAAUAUUAGUUACGUUUCGAGCUGCAGUGGCAAGCUUCAGUAGUUAGAA
.........(((.((((((((((((.((((.(.((....)).).))))(-(((..(((((((....)))))))..)))).)))).))))))))))).............. ( -35.70)
>DroSec_CAF1 42026 109 + 1
AAGACCAGUGCUCUACCACUGAGCUAAAGAGGCUCACAUGAACUUCUGG-AAAAAUAACUAAAAUAUUAGUUACGUUUCGAGCUGCAGUGGCAAGUUACAGUAGUGGGAA
....(((.((((((.((((((((((..(((((.((....)).))))).(-(((..(((((((....)))))))..)))).)))).))))))..))....)))).)))... ( -35.50)
>DroSim_CAF1 44277 109 + 1
AAGACCAGUGCUCUACCACUGAGCUAAAGAGGCUCACAUGAACUACUUG-AAAAAUAACUAAAAUAUUAGUUACGUUUCGAGCUGCAGUGGCAAGUUACAGUAGUUGGAA
....((((((((((.((((((((((.....)))))..........((((-(((..(((((((....)))))))..)))))))....)))))..))....)))).)))).. ( -30.10)
>DroEre_CAF1 42101 109 + 1
AAGACCAGUGCUCUGCCACUGAGCUAAAGAGGCUCACAUGAACGACUUG-AAAGAAAACCAAAAUAUUAGUUACGUUUCGAGCUCCAGUGGCAAGUUCCAGAAGUCAGAA
..(((....(((.((((((((((((...(((((((....))..((((..-..................))))..))))).)))).))))))))))).......))).... ( -27.95)
>DroYak_CAF1 41554 109 + 1
AAGACCAGUGCUCUGCCACUGAGCUAAAGAGGCUCACAUGAACGACUUG-AAAAAUAACCAAAAUAUUAGUUACGUAUCGAGCAUCAGUGGCAAGUUCCAGUAGUCAGAA
..(((.(.((..(((((((((((((.....)))))........(.((((-(.(..((((..........))))..).))))))...)))))).))...)).).))).... ( -27.00)
>DroPer_CAF1 73848 90 + 1
AAGACCAGUGCUCUGCCACUGAGCUAAGGAGGCUUGCUUGAAAAGAACGCACCAUCAAGCAAUAUAAAAGUUAGCUUCAGAG--GCAGUAGC------------------
.........((((((((.(((((((((......((((((((.............))))))))........))))).)))).)--)))).)))------------------ ( -29.36)
>consensus
AAGACCAGUGCUCUGCCACUGAGCUAAAGAGGCUCACAUGAACGACUUG_AAAAAUAACCAAAAUAUUAGUUACGUUUCGAGCUGCAGUGGCAAGUUACAGUAGUCAGAA
.....(((((......))))).((((..(.(((((..((((((..........................))).)))...))))).)..)))).................. (-13.73 = -14.62 +   0.89)

alignment

secondary structure

dotplot

Window 7

Location	8,148,323 – 8,148,432
Length	109
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	81.10
Mean single sequence MFE	-36.19
Consensus MFE	-19.70
Energy contribution	-20.70
Covariance contribution	1.00
Combinations/Pair	1.19
Mean z-score	-4.49
Structure conservation index	0.54
SVM decision value	1.92
SVM RNA-class probability	0.982681
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8148323 109 - 27905053
UUCUAACUACUGAAGCUUGCCACUGCAGCUCGAAACGUAACUAAUAUUUUAGUUAUUUUU-CAAGACGUUCAUGUGAGCCUCUUUAGCUCAGUGGCAGAGCACUGGUCUU
..............(((((((((((.((((.((((.((((((((....)))))))).)))-)((((.((((....)))).)))).)))))))))))).)))......... ( -39.20)
>DroSec_CAF1 42026 109 - 1
UUCCCACUACUGUAACUUGCCACUGCAGCUCGAAACGUAACUAAUAUUUUAGUUAUUUUU-CCAGAAGUUCAUGUGAGCCUCUUUAGCUCAGUGGUAGAGCACUGGUCUU
.....((((.(((...(((((((((.((((.((((.((((((((....)))))))).)))-).(((.((((....)))).)))..))))))))))))).))).))))... ( -35.50)
>DroSim_CAF1 44277 109 - 1
UUCCAACUACUGUAACUUGCCACUGCAGCUCGAAACGUAACUAAUAUUUUAGUUAUUUUU-CAAGUAGUUCAUGUGAGCCUCUUUAGCUCAGUGGUAGAGCACUGGUCUU
.....((((.(((...(((((((((.((((.((((.((((((((....)))))))).)))-)(((..((((....))))..))).))))))))))))).))).))))... ( -36.20)
>DroEre_CAF1 42101 109 - 1
UUCUGACUUCUGGAACUUGCCACUGGAGCUCGAAACGUAACUAAUAUUUUGGUUUUCUUU-CAAGUCGUUCAUGUGAGCCUCUUUAGCUCAGUGGCAGAGCACUGGUCUU
....((((..((....(((((((((.((((.((((...((((((....))))))...)))-)(((..((((....))))..))).)))))))))))))..))..)))).. ( -34.80)
>DroYak_CAF1 41554 109 - 1
UUCUGACUACUGGAACUUGCCACUGAUGCUCGAUACGUAACUAAUAUUUUGGUUAUUUUU-CAAGUCGUUCAUGUGAGCCUCUUUAGCUCAGUGGCAGAGCACUGGUCUU
....(((((.((....((((((((((.(((.((...((((((((....))))))))...)-)(((..((((....))))..))).)))))))))))))..)).))))).. ( -36.60)
>DroPer_CAF1 73848 90 - 1
------------------GCUACUGC--CUCUGAAGCUAACUUUUAUAUUGCUUGAUGGUGCGUUCUUUUCAAGCAAGCCUCCUUAGCUCAGUGGCAGAGCACUGGUCUU
------------------(((.((((--(.((((.(((((........((((((((.((......))..))))))))......))))))))).))))))))......... ( -34.84)
>consensus
UUCUAACUACUGGAACUUGCCACUGCAGCUCGAAACGUAACUAAUAUUUUAGUUAUUUUU_CAAGUCGUUCAUGUGAGCCUCUUUAGCUCAGUGGCAGAGCACUGGUCUU
................(((((((((.((((..(...((((((((....))))))))...........((((....))))...)..)))))))))))))............ (-19.70 = -20.70 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:51 2006