Locus 4360

Sequence ID X_DroMel_CAF1
Location 11,461,351 – 11,461,487
Length 136
Max. P 0.983880
window7162 window7163

overview

Window 2

Location 11,461,351 – 11,461,463
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.63
Mean single sequence MFE -32.00
Consensus MFE -22.08
Energy contribution -22.44
Covariance contribution 0.36
Combinations/Pair 1.36
Mean z-score -1.95
Structure conservation index 0.69
SVM decision value 0.68
SVM RNA-class probability 0.820274
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11461351 112 + 22224390
AAAAAU-AGGAACUGA-AGCUUUCGGCGCAAGCGCAAAGUGUU------GGAUAAGCAGAAGAGGAAGCAGAGCAGGUAGAGAGCAGGACAGCGGCACUAUCUAGCUGUCUCCCUCUUGC
......-.....(((.-.((((((.((....))......((((------.....)))).....))))))....)))...(((((..(((((((...........)))))))..))))).. ( -33.70)
>DroSec_CAF1 6749 111 + 1
AAAAA--AGGAACUGA-AGCUUUUGGCGCAAGCGCAAAGUGUU------GGAUAAGAAGAAGAGGAAGCGGAGCAGGUAGAGAGCAGGACAGCGCCACUAUCUAGCUAUCUCCUUCUUGA
.....--.....(..(-.(((((.(((....)).)))))).).------.).(((((((..((((.(((.....((((((.(.((......))..).)))))).))).))))))))))). ( -30.90)
>DroEre_CAF1 6534 110 + 1
AAAA---AACAACUGA-AGCUUUUGGCGCAAGCGCAAAGUGUU------GGAGAAGAUGAAGAAGAAGCAGAGCAGGUAGAGAGCAGGACAGCAACACUAUCUAGCUGUCUCCUUCCUGC
....---.....((..-((((((((((....)).))))).)))------..))..............((((.(.(((.(((.(((.(((.((.....)).))).))).)))))).))))) ( -30.90)
>DroYak_CAF1 6472 113 + 1
AAAAAGAAACAACUGA-AGCUUUUGGCGCAAGCGCAAAGUGUU------GGAGAAGAAGAAGAGGAAGCAGAGCAGGUAGAGAGCAGGAUAGCGACACUAUCUAGCUGUCUCCUUCUCGC
............((..-((((((((((....)).))))).)))------..))..............((.(((.(((.(((.(((.((((((.....)))))).))).)))))).))))) ( -34.40)
>DroAna_CAF1 9971 119 + 1
AUAAAAAAAUAUCUGAAAGCUUGGGGCGCAAGCGCAAAGUGAUAUGGAAGAAGAAGAAGAAGAGGGAGCAGGGCAGGUAGCAAGUGAGAUGGCAAUA-UCUCUAGUUCUCUCCCACUCUC
........(((((.....((((.(.((....)).).)))))))))............(((.(.(((((.(((((.(....)....((((((....))-))))..)))))))))).)))). ( -30.10)
>consensus
AAAAA__AACAACUGA_AGCUUUUGGCGCAAGCGCAAAGUGUU______GGAGAAGAAGAAGAGGAAGCAGAGCAGGUAGAGAGCAGGACAGCGACACUAUCUAGCUGUCUCCUUCUUGC
............(((...((((((.((....))((.....)).....................))))))....)))...(((((..(((((((...........)))))))..))))).. (-22.08 = -22.44 +   0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,461,389 – 11,461,487
Length 98
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 76.12
Mean single sequence MFE -26.56
Consensus MFE -17.86
Energy contribution -18.62
Covariance contribution 0.76
Combinations/Pair 1.21
Mean z-score -2.18
Structure conservation index 0.67
SVM decision value 1.96
SVM RNA-class probability 0.983880
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11461389 98 - 22224390
UUAAAAA--------UA--------ACUGAAAGAGUGAUCGCAAGAGGGAGACAGCUAGAUAGUGCCGCUGUCCUGCUCUCUACCUGCUCUGCUUCCUCUUCUGCUUAUCC------AAC
......(--------((--------(.(..(((((.((..((((((((.(((.(((..(((((.....)))))..))).))).))).)).))).)))))))..).))))..------... ( -26.70)
>DroSec_CAF1 6786 98 - 1
UUAAAAA--------UA--------ACUGAAAGAGUGAUCUCAAGAAGGAGAUAGCUAGAUAGUGGCGCUGUCCUGCUCUCUACCUGCUCCGCUUCCUCUUCUUCUUAUCC------AAC
.......--------..--------.....(((((.((.....((.((((((.(((..(((((.....)))))..))).))).))).)).....)))))))..........------... ( -22.60)
>DroEre_CAF1 6570 98 - 1
UUAAAAA--------UA--------AAUGAAAGAGCGAUCGCAGGAAGGAGACAGCUAGAUAGUGUUGCUGUCCUGCUCUCUACCUGCUCUGCUUCUUCUUCAUCUUCUCC------AAC
.......--------..--------...(((..((((...(((((.(((((.(((...(((((.....))))))))))).)).)))))..))))..)))............------... ( -28.60)
>DroYak_CAF1 6511 98 - 1
AUAAAAA--------UA--------AAUGAAAGAGCGAUCGCGAGAAGGAGACAGCUAGAUAGUGUCGCUAUCCUGCUCUCUACCUGCUCUGCUUCCUCUUCUUCUUCUCC------AAC
.......--------..--------.....(((((.((..(((((.((((((.(((..(((((.....)))))..))).))).))).))).)).)))))))..........------... ( -27.70)
>DroAna_CAF1 10011 119 - 1
CUAAAAACAAAAAAAUAUGUUAAAAAAUGGACUGGCGAUCGAGAGUGGGAGAGAACUAGAGA-UAUUGCCAUCUCACUUGCUACCUGCCCUGCUCCCUCUUCUUCUUCUUCUUCCAUAUC
.....((((........)))).....(((((..((.((..(((((.(((((((.....((((-(......)))))....((.....)).)).))))).).))))..)).)).)))))... ( -27.20)
>consensus
UUAAAAA________UA________AAUGAAAGAGCGAUCGCAAGAAGGAGACAGCUAGAUAGUGUCGCUGUCCUGCUCUCUACCUGCUCUGCUUCCUCUUCUUCUUCUCC______AAC
............................((((((((..((....))((((((.(((..(((((.....)))))..))).))).))))))))..)))........................ (-17.86 = -18.62 +   0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:05 2006