Locus 6371

Sequence ID 3R_DroMel_CAF1
Location 16,715,728 – 16,715,921
Length 193
Max. P 0.997673
window10384 window10385 window10386

overview

Window 4

Location 16,715,728 – 16,715,827
Length 99
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.50
Mean single sequence MFE -24.85
Consensus MFE -10.40
Energy contribution -10.60
Covariance contribution 0.20
Combinations/Pair 1.09
Mean z-score -2.29
Structure conservation index 0.42
SVM decision value 1.23
SVM RNA-class probability 0.933995
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16715728 99 - 27905053
------CCCGACCUCAG-----UGG-ACAAACUACAAGCCAUUUUCUGUCGACCGGCCUUGGCUUUGUUUCAA---------CUUGAGCAGCCAAUGACAAAUUCACUUGUCACACAACA
------..((((...((-----(((-.(.........))))))....))))...(((....((((.((....)---------)..)))).)))..((((((......))))))....... ( -20.40)
>DroPse_CAF1 32533 105 - 1
------CCCUACCACUGCCCGUUGGCUCGUAAUACAUGCCAUUUUCAGUCUCCCGGCCUUGGCUUUGUUUCAA---------CUUGAGCCACCAGUGACAAAUUCACUUGUCACACAACA
------..............(.(((((((....(((.((((......(((....)))..))))..))).....---------..))))))).).(((((((......)))))))...... ( -27.00)
>DroYak_CAF1 43505 99 - 1
------CCCGACCUCAU-----CGG-ACAAAAUACAAGCCAUUUUCUGUCGUCCGGCCUUGGCUUUGUUUCAA---------CUUGAGCAGCCAAUGACAAAUUCACUUGUCACACAACA
------.((((.....)-----)))-.......(((((........((((((..(((....((((.((....)---------)..)))).))).))))))......)))))......... ( -19.74)
>DroAna_CAF1 28314 111 - 1
UACCAACCCCACCUCUGUUC--UGG-UCAUAC------CCAUUAGAUGUUGGGUGGCCUUGGCAUUGUUUCAAACCAGGCAGCUUGAGCAGCCAAUGACAAAUUCACUUGUCACACAACA
..((((..((((((....((--(((-(.....------..))))))....))))))..))))..((((.........(((.((....)).)))..((((((......)))))).)))).. ( -30.10)
>DroPer_CAF1 31683 105 - 1
------CCCUACCACUGCUCGUUGGCUCGUAAUACAUGCCAUUUUCAGUCUCCCGGCCUUGGCUUUGUUUCAA---------CUUGAGCCACCAGUGACAAAUUCACUUGUCACACAACA
------..............(.(((((((....(((.((((......(((....)))..))))..))).....---------..))))))).).(((((((......)))))))...... ( -27.00)
>consensus
______CCCGACCUCUG__C__UGG_UCAUAAUACAAGCCAUUUUCUGUCGCCCGGCCUUGGCUUUGUUUCAA_________CUUGAGCAGCCAAUGACAAAUUCACUUGUCACACAACA
.......................((............((((......(((....)))..)))).(((((.(((..........))))))))))..((((((......))))))....... (-10.40 = -10.60 +   0.20)

alignment

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secondary structure

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Window 5

Location 16,715,827 – 16,715,921
Length 94
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.69
Mean single sequence MFE -31.80
Consensus MFE -20.74
Energy contribution -21.14
Covariance contribution 0.40
Combinations/Pair 1.10
Mean z-score -2.75
Structure conservation index 0.65
SVM decision value 2.58
SVM RNA-class probability 0.995517
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16715827 94 + 27905053
---AGAAAUUUGAAUUUAUGUUGGGGCC----------CGCA--------AA----AAGGGAAAUACUUUCAUUUGGAGC-UGCCACAAAGCAUUUCCGCUUUGUGGCACACACAUAAUG
---............((((((((.((((----------((..--------..----((((......))))....))).))-)((((((((((......)))))))))).)).)))))).. ( -29.70)
>DroPse_CAF1 32638 109 + 1
---GAAAAUUUGAAUCCAUGUUUUGGGCACUUU---UUUGCACUAGCUGGAA----AAGGAAAAUGCUUUCAUUUGGAGC-UGCCACAAAGCAUUUCCGCUUUGUGGCACACACAUAAUG
---...........((((......(((((((((---(((((....)).))))----))).....))))).....))))(.-(((((((((((......)))))))))))).......... ( -31.30)
>DroYak_CAF1 43604 94 + 1
---UGAAAUUUGAAUUUAUGUUGGGGGC----------CGCA--------AA----AAGGGAAAUACUUUCAUUUGGAGC-UGCCACAAAGCAUUUCCGCUUUGUGGCACACACAUAAUG
---............((((((((..(((----------..((--------((----((((......))))..))))..))-)((((((((((......)))))))))).)).)))))).. ( -28.40)
>DroAna_CAF1 28425 112 + 1
UGGGAACAUUUGAAUUUAUGUUAGGACUAGUUUUCUUUCGCA--------UGGGUGGGGGAGAAUACUUUCAUAUGGAGCCUGCCACAAAGCAUUUCCGCUUUGUGGCACACACAUAAUG
.(((..(((.((((.....((....))..(((((((..(((.--------...)))..)))))))...)))).)))...)))((((((((((......))))))))))............ ( -37.40)
>DroPer_CAF1 31788 109 + 1
---GAAAAUUUGAAUCCAUGUUUUGGGCACUUU---UUUGCACUAGCUGGAA----AAGGGAAAUGCUUUCAUUUGGAGC-UGCCACAAAGCAUUUCCGCUUUGUGGCACACACAUAAUG
---...........((((......(((((((((---(((.((.....)).))----)))))...))))).....))))(.-(((((((((((......)))))))))))).......... ( -32.20)
>consensus
___GAAAAUUUGAAUUUAUGUUGGGGGCA_UUU___UUCGCA________AA____AAGGGAAAUACUUUCAUUUGGAGC_UGCCACAAAGCAUUUCCGCUUUGUGGCACACACAUAAUG
...............((((((......................................((((....))))..........(((((((((((......)))))))))))...)))))).. (-20.74 = -21.14 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,715,827 – 16,715,921
Length 94
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.69
Mean single sequence MFE -28.70
Consensus MFE -25.25
Energy contribution -24.53
Covariance contribution -0.72
Combinations/Pair 1.13
Mean z-score -2.91
Structure conservation index 0.88
SVM decision value 2.91
SVM RNA-class probability 0.997673
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16715827 94 - 27905053
CAUUAUGUGUGUGCCACAAAGCGGAAAUGCUUUGUGGCA-GCUCCAAAUGAAAGUAUUUCCCUU----UU--------UGCG----------GGCCCCAACAUAAAUUCAAAUUUCU---
..((((((...((((((((((((....))))))))))))-((((((((.(((.....)))....----))--------)).)----------)))....))))))............--- ( -29.90)
>DroPse_CAF1 32638 109 - 1
CAUUAUGUGUGUGCCACAAAGCGGAAAUGCUUUGUGGCA-GCUCCAAAUGAAAGCAUUUUCCUU----UUCCAGCUAGUGCAAA---AAAGUGCCCAAAACAUGGAUUCAAAUUUUC---
.....((.(.(((((((((((((....))))))))))))-.).)))..((((.(((((((..((----(....((....)))))---)))))))(((.....))).)))).......--- ( -27.60)
>DroYak_CAF1 43604 94 - 1
CAUUAUGUGUGUGCCACAAAGCGGAAAUGCUUUGUGGCA-GCUCCAAAUGAAAGUAUUUCCCUU----UU--------UGCG----------GCCCCCAACAUAAAUUCAAAUUUCA---
..((((((...((((((((((((....))))))))))))-(((.((((.(((.....)))....----))--------)).)----------)).....))))))............--- ( -27.80)
>DroAna_CAF1 28425 112 - 1
CAUUAUGUGUGUGCCACAAAGCGGAAAUGCUUUGUGGCAGGCUCCAUAUGAAAGUAUUCUCCCCCACCCA--------UGCGAAAGAAAACUAGUCCUAACAUAAAUUCAAAUGUUCCCA
..((((((((.((((((((((((....)))))))))))).))..........(((.((((..(.((....--------)).)..)))).))).......))))))............... ( -30.60)
>DroPer_CAF1 31788 109 - 1
CAUUAUGUGUGUGCCACAAAGCGGAAAUGCUUUGUGGCA-GCUCCAAAUGAAAGCAUUUCCCUU----UUCCAGCUAGUGCAAA---AAAGUGCCCAAAACAUGGAUUCAAAUUUUC---
.....((.(.(((((((((((((....))))))))))))-.).)))..((((.((((((...((----((...((....)))))---)))))))(((.....))).)))).......--- ( -27.60)
>consensus
CAUUAUGUGUGUGCCACAAAGCGGAAAUGCUUUGUGGCA_GCUCCAAAUGAAAGUAUUUCCCUU____UU________UGCGAA___AAA_UGCCCCAAACAUAAAUUCAAAUUUUC___
..((((((((.((((((((((((....)))))))))))).))...........(((......................)))..................))))))............... (-25.25 = -24.53 +  -0.72)

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 12:19:50 2006