Locus 51

Sequence ID 2R_DroMel_CAF1
Location 1,306,606 – 1,306,890
Length 284
Max. P 0.994509
window94 window95 window96 window97 window98 window99 window100

overview

Window 4

Location 1,306,606 – 1,306,720
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.44
Mean single sequence MFE -26.35
Consensus MFE -24.42
Energy contribution -24.43
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.68
Structure conservation index 0.93
SVM decision value 0.15
SVM RNA-class probability 0.607846
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1306606 114 - 20766785
AGCUGAAACUGAAGUUGAGGCAGACACUGAAGGUACAUUCAACAAAAGCGACA------GCGACAACAAAACAUGUGUCAACUGCCAGACAUCCUGAGCAAUAUUAAUAACACUCGGCGA
.(((((......((((((.(((.....((((......))))......((....------))............))).))))))(((((.....))).))..............))))).. ( -26.30)
>DroSec_CAF1 24986 114 - 1
AGCUGAAACUGAAGUUGAGGCAGACACUGAAGGUACAUUCAACAAAAGCGACA------GCGACAACAAAACAUGUGUCAACUGCCAGACAUCCUGAGCAAUAUUAAUAACACUCGGCGA
.(((((......((((((.(((.....((((......))))......((....------))............))).))))))(((((.....))).))..............))))).. ( -26.30)
>DroSim_CAF1 3977 114 - 1
AGCUGAAACUGAAGUUGAGGCAGACACUGAAGGUACAUUCAACAAAAGCGACA------GCGACAACAAAACAUGUGUCAACUGCCAGACAUCCUGAGCAAUAUUAAUAACACUCGGCGA
.(((((......((((((.(((.....((((......))))......((....------))............))).))))))(((((.....))).))..............))))).. ( -26.30)
>DroEre_CAF1 7800 120 - 1
AGCUGAAACUGAAGUUGAGGCAGACACUGAAGGUACAUUCAACAAAAGCGACAGCGACAGCGACAACAAAACAUGUGUCAACUGCCAGACAUCCUGAGCAAUAUUAAUAACACUCGGCGA
.(((((..(((..((((..((......((((......))))......))..))))..))).((((.((.....))))))...((((((.....))).))).............))))).. ( -26.50)
>consensus
AGCUGAAACUGAAGUUGAGGCAGACACUGAAGGUACAUUCAACAAAAGCGACA______GCGACAACAAAACAUGUGUCAACUGCCAGACAUCCUGAGCAAUAUUAAUAACACUCGGCGA
.(((((......((((((.(((.....((((......))))......((..........))............))).))))))(((((.....))).))..............))))).. (-24.42 = -24.43 +   0.00) 

alignment

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secondary structure

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Window 5

Location 1,306,646 – 1,306,736
Length 90
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.17
Mean single sequence MFE -23.07
Consensus MFE -16.38
Energy contribution -16.38
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.58
Structure conservation index 0.71
SVM decision value 0.12
SVM RNA-class probability 0.591342
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1306646 90 - 20766785
CUACGGCCAAA------------------------GCUGAAGCUGAAACUGAAGUUGAGGCAGACACUGAAGGUACAUUCAACAAAAGCGACA------GCGACAACAAAACAUGUGUCA
...((((....------------------------))))..(((..(((....)))..))).(((((((((......))))......((....------)).............))))). ( -20.60)
>DroSec_CAF1 25026 90 - 1
CUACGGCCAAC------------------------GCUGAAGCUGAAACUGAAGUUGAGGCAGACACUGAAGGUACAUUCAACAAAAGCGACA------GCGACAACAAAACAUGUGUCA
...((((....------------------------))))..(((..(((....)))..))).(((((((((......))))......((....------)).............))))). ( -20.50)
>DroSim_CAF1 4017 90 - 1
CUACGGCCAAC------------------------GCUGGAGCUGAAACUGAAGUUGAGGCAGACACUGAAGGUACAUUCAACAAAAGCGACA------GCGACAACAAAACAUGUGUCA
...........------------------------((((..(((.....((((((.....(((...))).....)).)))).....)))..))------))((((.((.....)))))). ( -20.90)
>DroEre_CAF1 7840 120 - 1
CUAUCGCCGAAGCUGAACCAGAAGCAGAAGCUGAAGCUGAAGCUGAAACUGAAGUUGAGGCAGACACUGAAGGUACAUUCAACAAAAGCGACAGCGACAGCGACAACAAAACAUGUGUCA
...........(((........)))....((((..((((..(((.....((((((.....(((...))).....)).)))).....)))..))))..))))((((.((.....)))))). ( -30.30)
>consensus
CUACGGCCAAA________________________GCUGAAGCUGAAACUGAAGUUGAGGCAGACACUGAAGGUACAUUCAACAAAAGCGACA______GCGACAACAAAACAUGUGUCA
...................................(((..((((........))))..))).(((((((((......))))......((..........)).............))))). (-16.38 = -16.38 +   0.00) 

alignment

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secondary structure

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Window 6

Location 1,306,720 – 1,306,810
Length 90
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.70
Mean single sequence MFE -20.35
Consensus MFE -12.54
Energy contribution -12.79
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.62
SVM decision value 0.51
SVM RNA-class probability 0.762958
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1306720 90 + 20766785
UCAGC------------------------UUUGGCCGUAGCUACAGC------UACAGCUACCAACUUCCCUUGUCCUGCCACGUGUAAGCUGACAUUUUUUCAUUACUACACAUUUCAA
(((((------------------------((((((.(((((....))------)))......(((......)))....)))).....))))))).......................... ( -18.80)
>DroSec_CAF1 25100 90 + 1
UCAGC------------------------GUUGGCCGUAGCUACAGC------UACAGCUACCAACUUCCCUUGUCCUGCCACGUGUAAGCUGACAUUUUUUCAUUACUACACAUUUCAA
(((((------------------------(.((((.(((((....))------))).)))).)..............(((.....))).))))).......................... ( -18.50)
>DroSim_CAF1 4091 96 + 1
CCAGC------------------------GUUGGCCGUAGCUACAGCUACAGCUACAGCUACCAACUUCCCUUGUCCUGCCACGUGUAAGCUGACAUUUUUUCAUUACUACACAUUUCAA
.((((------------------------(((((..(((((....)))))(((....))).)))))...........(((.....))).))))........................... ( -20.90)
>DroEre_CAF1 7920 113 + 1
UCAGCUUCAGCUUCUGCUUCUGGUUCAGCUUCGGCGAUAGCUACAGC-------ACAGCUACCAACUUCCCUUGUCCUGCCACGUGUAAGCUGACAUUUUUUCAUUACUACACAUUUCAA
((((((((((((..((((..(((((..((....))...))))).)))-------).))))..(((......)))...........).))))))).......................... ( -23.20)
>consensus
UCAGC________________________GUUGGCCGUAGCUACAGC______UACAGCUACCAACUUCCCUUGUCCUGCCACGUGUAAGCUGACAUUUUUUCAUUACUACACAUUUCAA
................................(((.((((((..............))))))(((......)))....)))..(((((...(((.......)))....)))))....... (-12.54 = -12.79 +   0.25) 

alignment

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secondary structure

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dotplot

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Window 7

Location 1,306,720 – 1,306,810
Length 90
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.70
Mean single sequence MFE -27.62
Consensus MFE -20.54
Energy contribution -20.60
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -2.13
Structure conservation index 0.74
SVM decision value 1.16
SVM RNA-class probability 0.924221
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1306720 90 - 20766785
UUGAAAUGUGUAGUAAUGAAAAAAUGUCAGCUUACACGUGGCAGGACAAGGGAAGUUGGUAGCUGUA------GCUGUAGCUACGGCCAAA------------------------GCUGA
(((..((((((((...(((.......)))..))))))))..))).........((((....((((((------((....))))))))...)------------------------))).. ( -26.20)
>DroSec_CAF1 25100 90 - 1
UUGAAAUGUGUAGUAAUGAAAAAAUGUCAGCUUACACGUGGCAGGACAAGGGAAGUUGGUAGCUGUA------GCUGUAGCUACGGCCAAC------------------------GCUGA
(((..((((((((...(((.......)))..))))))))..)))..........((((...((((((------((....))))))))))))------------------------..... ( -26.70)
>DroSim_CAF1 4091 96 - 1
UUGAAAUGUGUAGUAAUGAAAAAAUGUCAGCUUACACGUGGCAGGACAAGGGAAGUUGGUAGCUGUAGCUGUAGCUGUAGCUACGGCCAAC------------------------GCUGG
(((..((((((((...(((.......)))..))))))))..)))..........(((((((((((((((....)))))))))...))))))------------------------..... ( -29.40)
>DroEre_CAF1 7920 113 - 1
UUGAAAUGUGUAGUAAUGAAAAAAUGUCAGCUUACACGUGGCAGGACAAGGGAAGUUGGUAGCUGU-------GCUGUAGCUAUCGCCGAAGCUGAACCAGAAGCAGAAGCUGAAGCUGA
..........................(((((((.....((((..(((.......)))((((((((.-------....)))))))))))))))))))..(((.(((....)))....))). ( -28.20)
>consensus
UUGAAAUGUGUAGUAAUGAAAAAAUGUCAGCUUACACGUGGCAGGACAAGGGAAGUUGGUAGCUGUA______GCUGUAGCUACGGCCAAA________________________GCUGA
.....((((((((...(((.......)))..))))))))(((..(((.......))).(((((((((........))))))))).)))................................ (-20.54 = -20.60 +   0.06) 

alignment

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secondary structure

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Window 8

Location 1,306,736 – 1,306,850
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.16
Mean single sequence MFE -28.02
Consensus MFE -25.59
Energy contribution -25.40
Covariance contribution -0.19
Combinations/Pair 1.07
Mean z-score -1.77
Structure conservation index 0.91
SVM decision value 0.66
SVM RNA-class probability 0.815584
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1306736 114 + 20766785
CUACAGC------UACAGCUACCAACUUCCCUUGUCCUGCCACGUGUAAGCUGACAUUUUUUCAUUACUACACAUUUCAAUAGCAGGGACACCCGUAGCCGCAUCAGUCGGCUACGAAGA
....(((------....))).....((((...((((((((...(((((...(((.......)))....)))))((....)).))).)))))...((((((((....).))))))))))). ( -29.00)
>DroSec_CAF1 25116 114 + 1
CUACAGC------UACAGCUACCAACUUCCCUUGUCCUGCCACGUGUAAGCUGACAUUUUUUCAUUACUACACAUUUCAAUAGCAGGGACACCCGUAGCCGCAUCAGCCAGCUGCGAAGA
....(((------....))).....((((...((((((((...(((((...(((.......)))....)))))((....)).))).)))))...(((((.((....))..))))))))). ( -24.90)
>DroSim_CAF1 4107 120 + 1
CUACAGCUACAGCUACAGCUACCAACUUCCCUUGUCCUGCCACGUGUAAGCUGACAUUUUUUCAUUACUACACAUUUCAAUAGCAGGGACACCCGUAGCCGCAUCAGCCGGCUGCGAAGA
....((((........)))).....((((...((((((((...(((((...(((.......)))....)))))((....)).))).)))))...((((((((....).))))))))))). ( -29.70)
>DroEre_CAF1 7960 113 + 1
CUACAGC-------ACAGCUACCAACUUCCCUUGUCCUGCCACGUGUAAGCUGACAUUUUUUCAUUACUACACAUUUCAAUAGCAGGGACACCCGUAGCCGCAUCAGCCGGCUACGAGGA
....(((-------...)))............((((((((...(((((...(((.......)))....)))))((....)).))).)))))(((((((((((....).)))))))).)). ( -28.50)
>consensus
CUACAGC______UACAGCUACCAACUUCCCUUGUCCUGCCACGUGUAAGCUGACAUUUUUUCAUUACUACACAUUUCAAUAGCAGGGACACCCGUAGCCGCAUCAGCCGGCUACGAAGA
.........................((((...((((((((...(((((...(((.......)))....)))))((....)).))).)))))...((((((((....).))))))))))). (-25.59 = -25.40 +  -0.19) 

alignment

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secondary structure

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dotplot

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Window 9

Location 1,306,736 – 1,306,850
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.16
Mean single sequence MFE -42.48
Consensus MFE -41.19
Energy contribution -41.20
Covariance contribution 0.00
Combinations/Pair 1.03
Mean z-score -2.93
Structure conservation index 0.97
SVM decision value 2.49
SVM RNA-class probability 0.994509
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1306736 114 - 20766785
UCUUCGUAGCCGACUGAUGCGGCUACGGGUGUCCCUGCUAUUGAAAUGUGUAGUAAUGAAAAAAUGUCAGCUUACACGUGGCAGGACAAGGGAAGUUGGUAGCUGUA------GCUGUAG
..((((((((((.(....)))))))))))..(((((....(((..((((((((...(((.......)))..))))))))..)))....)))))......((((....------))))... ( -38.80)
>DroSec_CAF1 25116 114 - 1
UCUUCGCAGCUGGCUGAUGCGGCUACGGGUGUCCCUGCUAUUGAAAUGUGUAGUAAUGAAAAAAUGUCAGCUUACACGUGGCAGGACAAGGGAAGUUGGUAGCUGUA------GCUGUAG
.....(((((((((....))((((((.((..(((((....(((..((((((((...(((.......)))..))))))))..)))....)))))..)).)))))).))------))))).. ( -43.40)
>DroSim_CAF1 4107 120 - 1
UCUUCGCAGCCGGCUGAUGCGGCUACGGGUGUCCCUGCUAUUGAAAUGUGUAGUAAUGAAAAAAUGUCAGCUUACACGUGGCAGGACAAGGGAAGUUGGUAGCUGUAGCUGUAGCUGUAG
.....((((((((((...((((((((.((..(((((....(((..((((((((...(((.......)))..))))))))..)))....)))))..)).)))))))))))))..))))).. ( -48.30)
>DroEre_CAF1 7960 113 - 1
UCCUCGUAGCCGGCUGAUGCGGCUACGGGUGUCCCUGCUAUUGAAAUGUGUAGUAAUGAAAAAAUGUCAGCUUACACGUGGCAGGACAAGGGAAGUUGGUAGCUGU-------GCUGUAG
..........((((....((((((((.((..(((((....(((..((((((((...(((.......)))..))))))))..)))....)))))..)).))))))))-------))))... ( -39.40)
>consensus
UCUUCGCAGCCGGCUGAUGCGGCUACGGGUGUCCCUGCUAUUGAAAUGUGUAGUAAUGAAAAAAUGUCAGCUUACACGUGGCAGGACAAGGGAAGUUGGUAGCUGUA______GCUGUAG
.....(((((.......(((((((((.((..(((((....(((..((((((((...(((.......)))..))))))))..)))....)))))..)).)))))))))......))))).. (-41.19 = -41.20 +   0.00) 

alignment

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secondary structure

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dotplot

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Window 0

Location 1,306,770 – 1,306,890
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.36
Mean single sequence MFE -40.90
Consensus MFE -39.25
Energy contribution -39.38
Covariance contribution 0.12
Combinations/Pair 1.05
Mean z-score -1.95
Structure conservation index 0.96
SVM decision value 0.81
SVM RNA-class probability 0.857374
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1306770 120 - 20766785
AUACACGAUAGGGGAAGUAGCAACAGCUGCUCGGCAGAGUUCUUCGUAGCCGACUGAUGCGGCUACGGGUGUCCCUGCUAUUGAAAUGUGUAGUAAUGAAAAAAUGUCAGCUUACACGUG
.....((((((((((((((((....))))))...........((((((((((.(....)))))))))))..))))..))))))..((((((((...(((.......)))..)))))))). ( -41.10)
>DroSec_CAF1 25150 120 - 1
AUGCACGAUAGGGGAAGUAGCAACAGCUGCUCGGCAGAGUUCUUCGCAGCUGGCUGAUGCGGCUACGGGUGUCCCUGCUAUUGAAAUGUGUAGUAAUGAAAAAAUGUCAGCUUACACGUG
.....((((((((((.(((((..(((((((..((.((....)))))))))))((....)).))))).....))))..))))))..((((((((...(((.......)))..)))))))). ( -39.90)
>DroSim_CAF1 4147 120 - 1
AUACACGAUAGGGGAAGUAGCAACAGCUGCUCGGCAGAGUUCUUCGCAGCCGGCUGAUGCGGCUACGGGUGUCCCUGCUAUUGAAAUGUGUAGUAAUGAAAAAAUGUCAGCUUACACGUG
.....((((((((((.(((((..((...((.((((.(((...)))...))))))...))..))))).....))))..))))))..((((((((...(((.......)))..)))))))). ( -38.60)
>DroEre_CAF1 7993 120 - 1
ACACACGAUAGGGGAAGUAGCAACAGCUGCUCGGCAGAGUUCCUCGUAGCCGGCUGAUGCGGCUACGGGUGUCCCUGCUAUUGAAAUGUGUAGUAAUGAAAAAAUGUCAGCUUACACGUG
.(((.((((((((((((((((....))))))...........((((((((((.(....)))))))))))..))))..))))))....((((((...(((.......)))..))))))))) ( -44.00)
>consensus
AUACACGAUAGGGGAAGUAGCAACAGCUGCUCGGCAGAGUUCUUCGCAGCCGGCUGAUGCGGCUACGGGUGUCCCUGCUAUUGAAAUGUGUAGUAAUGAAAAAAUGUCAGCUUACACGUG
.....((((((((((((((((....))))))...........((((((((((.(....)))))))))))..))))..))))))..((((((((...(((.......)))..)))))))). (-39.25 = -39.38 +   0.12) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:24:54 2006