Locus 2401

Sequence ID 3L_DroMel_CAF1
Location 6,754,238 – 6,754,562
Length 324
Max. P 0.999932
window3702 window3703 window3704 window3705 window3706

overview

Window 2

Location 6,754,238 – 6,754,342
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.43
Mean single sequence MFE -26.35
Consensus MFE -22.34
Energy contribution -22.45
Covariance contribution 0.11
Combinations/Pair 1.10
Mean z-score -1.56
Structure conservation index 0.85
SVM decision value 0.02
SVM RNA-class probability 0.541220
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6754238 104 - 23771897
UAUGCCCCGAUAUCGGAUCGGCAUCUCCCUCGCUUCUGGCUAGGCAUUCGUAUGUUACAUGGAGAUGUAAGAAUUCCAU--------UUUUGAUUUUAAUCAAUAGAAUCGC--------
.......((((.(((((...((((((((((.((.....)).))((((....)))).....))))))))......)))..--------..(((((....)))))..)))))).-------- ( -24.30)
>DroSec_CAF1 17214 104 - 1
UAUGCCCCAAUAUCGGAUCGGCAUCUCCCUCGCUUCUGGCUAGGCAUUCGUAUGUUACAUGGAGAUGUAAGAAUUCCAU--------UUUUGAUUUUAAUCAAUAGAAUCGC--------
..............(((...((((((((((.((.....)).))((((....)))).....))))))))......)))..--------....(((((((.....)))))))..-------- ( -23.40)
>DroSim_CAF1 17544 104 - 1
UAUGCCCCGAUAUCGGAUCGGCAUCUCCCUCGCUUCUGGCUAGGCAUUUGUAUGUUACAUGGAGAUGUAAGAAUUCCAU--------UUUUGAUUUUAAUCAAUAGAAUCGC--------
.......((((.(((((...((((((((((.((.....)).))((((....)))).....))))))))......)))..--------..(((((....)))))..)))))).-------- ( -24.30)
>DroEre_CAF1 30128 104 - 1
UAUGCACCGAUAUCGGAUCGGCAUCUCCCUCGCUUCUGGCUAGGCAUUCGUAUGUUACAUGGAGAUGUAAAAAUUCCAU--------UUUUGAUUUUAAUCAAUAGAAUCGA--------
.......((((.(((((...((((((((((.((.....)).))((((....)))).....))))))))......)))..--------..(((((....)))))..)))))).-------- ( -25.00)
>DroYak_CAF1 19911 104 - 1
UAUGCCCCGAUAUCGGAUCGGCAUCUCCCUCGCUUCUGGCUAGGCAUUCGUAUGUUACAUGGAGAUGUAAAAAUACCAU--------UUUUGAUUUUAAUCAAUAGAAUCGA--------
......(((....)))....((((((((((.((.....)).))((((....)))).....))))))))...........--------..(((((((((.....)))))))))-------- ( -24.10)
>DroAna_CAF1 26679 119 - 1
UAUGGCCCGGUAUCGGGCCGGCAUCUCCCUCGCUUCUGGCUA-ACAUUCGAAUGUUACAUGGAGAUGUAUAAAUUCCAUUUUUUCAUUUUUGAUUUUAAUCAAUAGAAUCGCAAAUGCCC
..(((((((....)))))))((((((((...((.....))((-((((....))))))...))))))))................(((((.((((((((.....)))))))).)))))... ( -37.00)
>consensus
UAUGCCCCGAUAUCGGAUCGGCAUCUCCCUCGCUUCUGGCUAGGCAUUCGUAUGUUACAUGGAGAUGUAAAAAUUCCAU________UUUUGAUUUUAAUCAAUAGAAUCGC________
.......((((.(((((...((((((((...((.....))..(((((....)))))....))))))))......)))............(((((....)))))..))))))......... (-22.34 = -22.45 +   0.11)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,754,302 – 6,754,422
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 98.06
Mean single sequence MFE -35.93
Consensus MFE -33.88
Energy contribution -33.97
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -1.31
Structure conservation index 0.94
SVM decision value 1.34
SVM RNA-class probability 0.944212
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6754302 120 + 23771897
GCCAGAAGCGAGGGAGAUGCCGAUCCGAUAUCGGGGCAUAACUAUGUGCCAGACCAUUUCAUUUUUCAACAAUUGGCCAAAACUACGCCUCAAUAACCAAAACGGGGCGUGUGCGGCCAC
((.....))..(..((((((((((.....)))))((((((....)))))).........)))))..)......(((((...((.(((((((............)))))))))..))))). ( -40.20)
>DroSec_CAF1 17278 120 + 1
GCCAGAAGCGAGGGAGAUGCCGAUCCGAUAUUGGGGCAUAACUAUGUGCCAGACCAUUUCAUUUUUCAACAAUUGGCCAAAACUACGCCUCAAUAACCAAAACGGGGCGUGUGCUGCCAC
((.....))..(..((((((((((.....)))))((((((....)))))).........)))))..)......((((....((.(((((((............)))))))))...)))). ( -34.40)
>DroSim_CAF1 17608 120 + 1
GCCAGAAGCGAGGGAGAUGCCGAUCCGAUAUCGGGGCAUAACUAUGUGCCAGACCAUUUCAUUUUUCAACAAUUGGCCAAAACUACGCCUCAAUAACCAAAACGGGGCGUGUGCUGCCAC
((.....))..(..((((((((((.....)))))((((((....)))))).........)))))..)......((((....((.(((((((............)))))))))...)))). ( -36.50)
>DroEre_CAF1 30192 120 + 1
GCCAGAAGCGAGGGAGAUGCCGAUCCGAUAUCGGUGCAUAACUAUGUGCCAGACCAUUUCAUUUUUCAACAAUUGGCCAAAACUACGCCUCAAUAACCAAAACGGGGCGUGUGCUGCCAC
((.....))..(..(((((..(((.....)))((..(((....)))..)).........)))))..)......((((....((.(((((((............)))))))))...)))). ( -32.00)
>DroYak_CAF1 19975 120 + 1
GCCAGAAGCGAGGGAGAUGCCGAUCCGAUAUCGGGGCAUAACUAUGUGCCAGACCAUUUCAUUUUUCAACAAUUGGCCAAAACUACGCCUCAAUAACCAAAACGGGGCGUGUGCUGCCAC
((.....))..(..((((((((((.....)))))((((((....)))))).........)))))..)......((((....((.(((((((............)))))))))...)))). ( -36.50)
>DroAna_CAF1 26758 120 + 1
GCCAGAAGCGAGGGAGAUGCCGGCCCGAUACCGGGCCAUAACUAUGUGCCAGACCAUUUCAUUUUUCAACAAUUGGCCAAAACUACGCCUCAAUAACCAAAACGGGGCGUGUGCUGCCAC
((.....))..(..(((((..((((((....))))))........(((......)))..)))))..)......((((....((.(((((((............)))))))))...)))). ( -36.00)
>consensus
GCCAGAAGCGAGGGAGAUGCCGAUCCGAUAUCGGGGCAUAACUAUGUGCCAGACCAUUUCAUUUUUCAACAAUUGGCCAAAACUACGCCUCAAUAACCAAAACGGGGCGUGUGCUGCCAC
((.....))..(..((((((((((.....)))))((((((....)))))).........)))))..)......((((....((.(((((((............)))))))))...)))). (-33.88 = -33.97 +   0.08)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,754,342 – 6,754,462
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 96.82
Mean single sequence MFE -31.64
Consensus MFE -29.93
Energy contribution -30.10
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.51
Structure conservation index 0.95
SVM decision value 2.00
SVM RNA-class probability 0.985152
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6754342 120 + 23771897
ACUAUGUGCCAGACCAUUUCAUUUUUCAACAAUUGGCCAAAACUACGCCUCAAUAACCAAAACGGGGCGUGUGCGGCCACAAAAGUAAUGAGCAGUUGGCCACGCGCGCUCCCAGUAAAA
(((.((.(((((....................)))))))........................((((((((((.(((((.....((.....))...))))).))))))).)))))).... ( -32.15)
>DroSec_CAF1 17318 119 + 1
ACUAUGUGCCAGACCAUUUCAUUUUUCAACAAUUGGCCAAAACUACGCCUCAAUAACCAAAACGGGGCGUGUGCUGCCACAAAAGUAAUGAGCAGUUGGCCACGCGCGCUCCAAGUAAA-
(((..(((((.((.....)).............((((((....((((((((............)))))))).(((((((.........)).))))))))))).).))))....)))...- ( -31.00)
>DroSim_CAF1 17648 119 + 1
ACUAUGUGCCAGACCAUUUCAUUUUUCAACAAUUGGCCAAAACUACGCCUCAAUAACCAAAACGGGGCGUGUGCUGCCACAAAAGUAAUGAGCAGUUGGCCACGCGCGCUCCCAGUAAA-
(((..(((((.((.....)).............((((((....((((((((............)))))))).(((((((.........)).))))))))))).).))))....)))...- ( -31.00)
>DroEre_CAF1 30232 116 + 1
ACUAUGUGCCAGACCAUUUCAUUUUUCAACAAUUGGCCAAAACUACGCCUCAAUAACCAAAACGGGGCGUGUGCUGCCACAAAAGUAAUGAGCAGUUGGCCACGCGCGCUCCCAGU----
.....((((..((.....)).............((((((....((((((((............)))))))).(((((((.........)).))))))))))).)))).........---- ( -30.80)
>DroYak_CAF1 20015 120 + 1
ACUAUGUGCCAGACCAUUUCAUUUUUCAACAAUUGGCCAAAACUACGCCUCAAUAACCAAAACGGGGCGUGUGCUGCCACAAAAGUAAUGAGCAGUUGGCCACGCGCGCUCCCAGUCAAA
.....((((..((.....)).............((((((....((((((((............)))))))).(((((((.........)).))))))))))).))))............. ( -30.80)
>DroAna_CAF1 26798 119 + 1
ACUAUGUGCCAGACCAUUUCAUUUUUCAACAAUUGGCCAAAACUACGCCUCAAUAACCAAAACGGGGCGUGUGCUGCCACAAAAGUAAUGAGCAGUUGGCCACGCGCGCUCCGAGAGGG-
.....((((..((.....)).............((((((....((((((((............)))))))).(((((((.........)).))))))))))).))))...((....)).- ( -34.10)
>consensus
ACUAUGUGCCAGACCAUUUCAUUUUUCAACAAUUGGCCAAAACUACGCCUCAAUAACCAAAACGGGGCGUGUGCUGCCACAAAAGUAAUGAGCAGUUGGCCACGCGCGCUCCCAGUAAA_
.....((((..((.....)).............((((((....((((((((............)))))))).(((((((.........)).))))))))))).))))............. (-29.93 = -30.10 +   0.17)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,754,462 – 6,754,562
Length 100
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 90.41
Mean single sequence MFE -31.93
Consensus MFE -28.36
Energy contribution -29.12
Covariance contribution 0.76
Combinations/Pair 1.04
Mean z-score -4.34
Structure conservation index 0.89
SVM decision value 4.64
SVM RNA-class probability 0.999932
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6754462 100 + 23771897
AAAAAGAGGGGGGAAAAAAACAUUACCCGCAGGCGAACGAAA-AAAUAAA-AAACUGCAAAAGGAUGCAGUGAGUAGUGGAGUCUCUCUGGUUCGGCCUGCA
.......(((.(........)....)))((((((((((....-.......-..((((((......))))))(((.((......)))))..)))).)))))). ( -31.50)
>DroSec_CAF1 17437 98 + 1
--AAAGAGGGGGGAAA-AAACAUUACCCGCAGGCGAACGAAA-AAAUAAAAAAACUGCAGAAGGAUGCAUUGAGAAGUGGAGUCUCUCUGCUUCGGCCUGCA
--.....(((......-........)))((((((........-............((((......))))....((((..(((...)))..)))).)))))). ( -31.44)
>DroSim_CAF1 17767 98 + 1
--AAAGAGGGGGGAAAAAAACAUUACCCGCAGGCGAACGAAA-AAAUAAA-AAACUGCAGAAGGAUGCAGUGAGAAGUGGAGUCUCUCUGCUUCGGCCUGCA
--.....(((.(........)....)))((((((........-.......-..((((((......))))))..((((..(((...)))..)))).)))))). ( -36.20)
>DroEre_CAF1 30348 98 + 1
--AAAAAGGGGGA-AAAAAACAUUACCCGCAGGCGAACGAAAGAAAUAAA-AAACUGCAUAAGGAUGCAGCGAGAAGUGGAGUCUCUUUGCUACGGCCUGCG
--.....(((..(-........)..)))((((((...(....).......-...((((((....))))))...(.((..(((...)))..)).).)))))). ( -29.50)
>DroYak_CAF1 20135 99 + 1
UAAAAAAAGGGGG-AAAAAACAUUACCCGCAGGCGAACGAAA-ACAUAAA-AAACUGCAGAAGGAUGCAGCGAGAAGUGGAGUCGCUUUGCCUCGGCCUGCA
........(((..-...........)))((((((........-.......-...(((((......)))))(((((((((....)))))...)))))))))). ( -31.02)
>consensus
__AAAGAGGGGGGAAAAAAACAUUACCCGCAGGCGAACGAAA_AAAUAAA_AAACUGCAGAAGGAUGCAGUGAGAAGUGGAGUCUCUCUGCUUCGGCCUGCA
........(((..............)))((((((....................(((((......)))))...(((((((((...))))))))).)))))). (-28.36 = -29.12 +   0.76)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,754,462 – 6,754,562
Length 100
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 90.41
Mean single sequence MFE -27.56
Consensus MFE -23.88
Energy contribution -24.40
Covariance contribution 0.52
Combinations/Pair 1.14
Mean z-score -3.62
Structure conservation index 0.87
SVM decision value 4.38
SVM RNA-class probability 0.999884
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6754462 100 - 23771897
UGCAGGCCGAACCAGAGAGACUCCACUACUCACUGCAUCCUUUUGCAGUUU-UUUAUUU-UUUCGUUCGCCUGCGGGUAAUGUUUUUUUCCCCCCUCUUUUU
.((((((.((((..(((((......)).)))((((((......))))))..-.......-....))))))))))(((.((......)).))).......... ( -30.10)
>DroSec_CAF1 17437 98 - 1
UGCAGGCCGAAGCAGAGAGACUCCACUUCUCAAUGCAUCCUUCUGCAGUUUUUUUAUUU-UUUCGUUCGCCUGCGGGUAAUGUUU-UUUCCCCCCUCUUU--
.(((((((((((..(((((.......)))))..((((......))))............-)))))...))))))(((.((.....-.)).))).......-- ( -25.00)
>DroSim_CAF1 17767 98 - 1
UGCAGGCCGAAGCAGAGAGACUCCACUUCUCACUGCAUCCUUCUGCAGUUU-UUUAUUU-UUUCGUUCGCCUGCGGGUAAUGUUUUUUUCCCCCCUCUUU--
.(((((((((((..(((((.......)))))((((((......))))))..-.......-)))))...))))))(((.((......)).)))........-- ( -28.60)
>DroEre_CAF1 30348 98 - 1
CGCAGGCCGUAGCAAAGAGACUCCACUUCUCGCUGCAUCCUUAUGCAGUUU-UUUAUUUCUUUCGUUCGCCUGCGGGUAAUGUUUUUU-UCCCCCUUUUU--
.((((((.(.(((...((((.......))))(((((((....)))))))..-............))))))))))(((.((......))-.))).......-- ( -27.90)
>DroYak_CAF1 20135 99 - 1
UGCAGGCCGAGGCAAAGCGACUCCACUUCUCGCUGCAUCCUUCUGCAGUUU-UUUAUGU-UUUCGUUCGCCUGCGGGUAAUGUUUUUU-CCCCCUUUUUUUA
.((((((.((.(.(((((((.......))..((((((......))))))..-.....))-)))).)).))))))(((.((......))-.)))......... ( -26.20)
>consensus
UGCAGGCCGAAGCAGAGAGACUCCACUUCUCACUGCAUCCUUCUGCAGUUU_UUUAUUU_UUUCGUUCGCCUGCGGGUAAUGUUUUUUUCCCCCCUCUUU__
.(((((((((((.(((((((.......))))((((((......)))))).......))).)))))...))))))(((.((......)).))).......... (-23.88 = -24.40 +   0.52)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:26 2006