Locus 7911

Sequence ID 3L_DroMel_CAF1
Location 21,051,898 – 21,052,176
Length 278
Max. P 0.998709
window12892 window12893 window12894 window12895 window12896 window12897

overview

Window 2

Location 21,051,898 – 21,052,017
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.15
Mean single sequence MFE -23.42
Consensus MFE -19.98
Energy contribution -20.18
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.85
SVM decision value 0.49
SVM RNA-class probability 0.757616
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21051898 119 + 23771897
AGUUUUUGGUCU-UUGAAAACGUCAUCGUGUCGCAGAUAAAAUAACAAACAAACACCGGCCCCCAAAAAAGAAAAACAGACAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAAU
.......(((((-(((.....((((((........)))...................((...))..............)))......))))))))...(((((((....))))))).... ( -24.50)
>DroSec_CAF1 107048 119 + 1
AGUUUUUGGUCUUUUGAAAACGUCAUCGUGUCGCAGAUAAAAUAACAAACAAACACCGGCCCCCAAAAAAGAAAAACAGACAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAA-
.(((((..(....)..)))))(.(((..((((.........................((...))......(.....).))))..))))..........(((((((....)))))))...- ( -21.80)
>DroSim_CAF1 13261 119 + 1
AGUUUUUGGUCUUUUGAAAACGUCAUCGUGUCGCAGAUAAAAUAACAAACAAACACCGGCCCCCAAAAAAGAAAAACAAACAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAA-
.((((((..((((((......(((...((((.....................)))).)))......))))))..)).)))).................(((((((....)))))))...- ( -20.90)
>DroEre_CAF1 29470 118 + 1
AGUUUUUGGUCU-UUGAAAACGUCAUCGUGUCGCAGAUAAAAUAACAAACAAACACCGGCCCCCAAAAAAGAAAAACAGACAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAA-
.......(((((-(((.....((((((........)))...................((...))..............)))......))))))))...(((((((....)))))))...- ( -24.50)
>DroYak_CAF1 526 117 + 1
AGUUUUUGGUCU-UUGAAAACGUCAUCGUGUCGCAGACAAAAUAACAAACAAACACCGGCCCCCAA-AAAGAAAAACAGACAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAA-
.......(((((-(((.....(((....((((...))))..................((...))..-...........)))......))))))))...(((((((....)))))))...- ( -25.40)
>consensus
AGUUUUUGGUCU_UUGAAAACGUCAUCGUGUCGCAGAUAAAAUAACAAACAAACACCGGCCCCCAAAAAAGAAAAACAGACAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAA_
.(((((..(....)..)))))(.(((..((((.........................((...))......(.....).))))..))))..........(((((((....))))))).... (-19.98 = -20.18 +   0.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,051,937 – 21,052,056
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.61
Mean single sequence MFE -23.26
Consensus MFE -21.04
Energy contribution -21.24
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.23
Structure conservation index 0.90
SVM decision value 3.20
SVM RNA-class probability 0.998709
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21051937 119 + 23771897
AAUAACAAACAAACACCGGCCCCCAAAAAAGAAAAACAGACAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAAUAUCUCAUCUCCUGCGUUUUCCCAGGCUCAAAGGAAAAA-A
...............((((((..(......).......(..((((((((.((((....(((((((....))))))).........))))..))))))))..).))))....)).....-. ( -20.92)
>DroSec_CAF1 107088 117 + 1
AAUAACAAACAAACACCGGCCCCCAAAAAAGAAAAACAGACAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAA--UCUCAUCUGCUGCGUUUUCUCAGGCUCAAAGGAAAAA-A
...............((((((..(......).......((.((((((((.((((....(((((((....)))))))...--....))))..)))))))).)).))))....)).....-. ( -25.70)
>DroSim_CAF1 13301 117 + 1
AAUAACAAACAAACACCGGCCCCCAAAAAAGAAAAACAAACAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAA--UCUCAUCUGCUGCGUUUUCCCAGGCUCAAAGGAAAAA-A
...............((((((..(......)..........((((((((.((((....(((((((....)))))))...--....))))..))))))))....))))....)).....-. ( -23.00)
>DroEre_CAF1 29509 117 + 1
AAUAACAAACAAACACCGGCCCCCAAAAAAGAAAAACAGACAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAA--UCUCAUCUGCUGCGUU-UCUCAGGCUCAAAGGAAACGAG
.................((((..(......).......((..(((((((.((((....(((((((....)))))))...--....))))..))))))-).)).))))....(....)... ( -23.60)
>DroYak_CAF1 565 117 + 1
AAUAACAAACAAACACCGGCCCCCAA-AAAGAAAAACAGACAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAA--UCUCAUCUGCUGCGUUUUCCCAGGCUCAAAGGAAAAGAG
...............((((((.....-...(.....).(..((((((((.((((....(((((((....)))))))...--....))))..))))))))..).))))....))....... ( -23.10)
>consensus
AAUAACAAACAAACACCGGCCCCCAAAAAAGAAAAACAGACAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAA__UCUCAUCUGCUGCGUUUUCCCAGGCUCAAAGGAAAAA_A
...............((((((..(......)..........((((((((.((((....(((((((....))))))).........))))..))))))))....))))....))....... (-21.04 = -21.24 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,051,937 – 21,052,056
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.61
Mean single sequence MFE -33.06
Consensus MFE -29.20
Energy contribution -29.40
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -1.93
Structure conservation index 0.88
SVM decision value 2.16
SVM RNA-class probability 0.989239
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21051937 119 - 23771897
U-UUUUUCCUUUGAGCCUGGGAAAACGCAGGAGAUGAGAUAUUUGGCUGACAUCAAUCAGCCGGAGAUCUUUGCAUUUUGUCUGUUUUUCUUUUUUGGGGGCCGGUGUUUGUUUGUUAUU
.-.....((((..((...(((((((((.(.((((((((((.(((((((((......))))))))).))))...)))))).).)))))))))..))..))))................... ( -34.60)
>DroSec_CAF1 107088 117 - 1
U-UUUUUCCUUUGAGCCUGAGAAAACGCAGCAGAUGAGA--UUUGGCUGACAUCAAUCAGCCGGAGAUCUUUGCAUUUUGUCUGUUUUUCUUUUUUGGGGGCCGGUGUUUGUUUGUUAUU
.-.....((((..((...(((((((.((((((((.((((--(((((((((......)))))))..)))))).....)))).))))))))))).))..))))................... ( -31.90)
>DroSim_CAF1 13301 117 - 1
U-UUUUUCCUUUGAGCCUGGGAAAACGCAGCAGAUGAGA--UUUGGCUGACAUCAAUCAGCCGGAGAUCUUUGCAUUUUGUUUGUUUUUCUUUUUUGGGGGCCGGUGUUUGUUUGUUAUU
.-.....((((..((...((((((((((((((((.((..--(((((((((......)))))))))..)))))))....)))..))))))))..))..))))................... ( -32.90)
>DroEre_CAF1 29509 117 - 1
CUCGUUUCCUUUGAGCCUGAGA-AACGCAGCAGAUGAGA--UUUGGCUGACAUCAAUCAGCCGGAGAUCUUUGCAUUUUGUCUGUUUUUCUUUUUUGGGGGCCGGUGUUUGUUUGUUAUU
.(((...((((..((...((((-((.((((((((.((((--(((((((((......)))))))..)))))).....)))).)))).)))))).))..)))).)))............... ( -33.40)
>DroYak_CAF1 565 117 - 1
CUCUUUUCCUUUGAGCCUGGGAAAACGCAGCAGAUGAGA--UUUGGCUGACAUCAAUCAGCCGGAGAUCUUUGCAUUUUGUCUGUUUUUCUUU-UUGGGGGCCGGUGUUUGUUUGUUAUU
.......((((..((...((((((((((((((((.((..--(((((((((......)))))))))..)))))))....)))..)))))))).)-)..))))................... ( -32.50)
>consensus
U_UUUUUCCUUUGAGCCUGGGAAAACGCAGCAGAUGAGA__UUUGGCUGACAUCAAUCAGCCGGAGAUCUUUGCAUUUUGUCUGUUUUUCUUUUUUGGGGGCCGGUGUUUGUUUGUUAUU
.......((((..((...(((((((.((((((((.((((..(((((((((......)))))))))..)))).....)))).))))))))))).))..))))................... (-29.20 = -29.40 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,051,977 – 21,052,096
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.35
Mean single sequence MFE -24.97
Consensus MFE -21.96
Energy contribution -22.16
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.51
Structure conservation index 0.88
SVM decision value 1.08
SVM RNA-class probability 0.912179
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21051977 119 + 23771897
CAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAAUAUCUCAUCUCCUGCGUUUUCCCAGGCUCAAAGGAAAAA-ACUUUUCUUCUCACUCGCUUCAAAGCUGAAUAAAAACACUU
.((((((((.((((....(((((((....))))))).........))))..)))))))).......((((((((((..-..))))))).......(((....))))))............ ( -22.02)
>DroSec_CAF1 107128 117 + 1
CAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAA--UCUCAUCUGCUGCGUUUUCUCAGGCUCAAAGGAAAAA-ACUUUUCUUCUCACUCGCUUCAAAGCUGAAUAAAUACACUU
.((((((((.((((....(((((((....)))))))...--....))))..)))))))).......((((((((((..-..))))))).......(((....))))))............ ( -24.30)
>DroSim_CAF1 13341 117 + 1
CAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAA--UCUCAUCUGCUGCGUUUUCCCAGGCUCAAAGGAAAAA-ACUUUUCUUCUCACUCGCUUCAAAGCUGAAUAAAUACACUU
.((((((((.((((....(((((((....)))))))...--....))))..)))))))).......((((((((((..-..))))))).......(((....))))))............ ( -24.30)
>DroEre_CAF1 29549 117 + 1
CAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAA--UCUCAUCUGCUGCGUU-UCUCAGGCUCAAAGGAAACGAGAUUUUCUUGUCACUCGCUUCAAAGCAGAAUAAAUACACUU
..................(((((((....)))))))...--.....((((((.((((-(((..........))))))).(((......)))...........))))))............ ( -27.50)
>DroYak_CAF1 604 118 + 1
CAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAA--UCUCAUCUGCUGCGUUUUCCCAGGCUCAAAGGAAAAGAGGUUUUCUUGUCACUCGCUUCAAAGCAGAAUAAAUACACUU
..................(((((((....)))))))...--.....((((((...((((((..........))))))(((((.............)))))..))))))............ ( -26.72)
>consensus
CAAAAUGCAAAGAUCUCCGGCUGAUUGAUGUCAGCCAAA__UCUCAUCUGCUGCGUUUUCCCAGGCUCAAAGGAAAAA_ACUUUUCUUCUCACUCGCUUCAAAGCUGAAUAAAUACACUU
.((((((((.((((....(((((((....))))))).........))))..))))))))..........(((((((.....))))))).......(((....)))............... (-21.96 = -22.16 +   0.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 21,051,977 – 21,052,096
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.35
Mean single sequence MFE -36.42
Consensus MFE -29.22
Energy contribution -30.02
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.68
Structure conservation index 0.80
SVM decision value 2.06
SVM RNA-class probability 0.986954
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21051977 119 - 23771897
AAGUGUUUUUAUUCAGCUUUGAAGCGAGUGAGAAGAAAAGU-UUUUUCCUUUGAGCCUGGGAAAACGCAGGAGAUGAGAUAUUUGGCUGACAUCAAUCAGCCGGAGAUCUUUGCAUUUUG
...(.(((((((((.(((....)))))))))))).)...((-.(((((((........))))))).))..((((((((((.(((((((((......))))))))).))))...)))))). ( -36.00)
>DroSec_CAF1 107128 117 - 1
AAGUGUAUUUAUUCAGCUUUGAAGCGAGUGAGAAGAAAAGU-UUUUUCCUUUGAGCCUGAGAAAACGCAGCAGAUGAGA--UUUGGCUGACAUCAAUCAGCCGGAGAUCUUUGCAUUUUG
..((((.(((.(((((.((..(((.....(((((((....)-)))))))))..)).)))))))))))).(((((.((..--(((((((((......)))))))))..)))))))...... ( -35.70)
>DroSim_CAF1 13341 117 - 1
AAGUGUAUUUAUUCAGCUUUGAAGCGAGUGAGAAGAAAAGU-UUUUUCCUUUGAGCCUGGGAAAACGCAGCAGAUGAGA--UUUGGCUGACAUCAAUCAGCCGGAGAUCUUUGCAUUUUG
..((((.(((((((.(((....)))))))))).........-..((((((........)))))))))).(((((.((..--(((((((((......)))))))))..)))))))...... ( -36.80)
>DroEre_CAF1 29549 117 - 1
AAGUGUAUUUAUUCUGCUUUGAAGCGAGUGACAAGAAAAUCUCGUUUCCUUUGAGCCUGAGA-AACGCAGCAGAUGAGA--UUUGGCUGACAUCAAUCAGCCGGAGAUCUUUGCAUUUUG
..((((.(((.....((((.((((((((............))))))))....))))...)))-.)))).(((((.((..--(((((((((......)))))))))..)))))))...... ( -37.80)
>DroYak_CAF1 604 118 - 1
AAGUGUAUUUAUUCUGCUUUGAAGCGAGUGACAAGAAAACCUCUUUUCCUUUGAGCCUGGGAAAACGCAGCAGAUGAGA--UUUGGCUGACAUCAAUCAGCCGGAGAUCUUUGCAUUUUG
..((((..((((((.(((....))))))))).............((((((........)))))))))).(((((.((..--(((((((((......)))))))))..)))))))...... ( -35.80)
>consensus
AAGUGUAUUUAUUCAGCUUUGAAGCGAGUGAGAAGAAAAGU_UUUUUCCUUUGAGCCUGGGAAAACGCAGCAGAUGAGA__UUUGGCUGACAUCAAUCAGCCGGAGAUCUUUGCAUUUUG
..((((..((((((.(((....))))))))).............((((((........)))))))))).(((((.((....(((((((((......)))))))))..)))))))...... (-29.22 = -30.02 +   0.80)

alignment

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secondary structure

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dotplot

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Window 7

Location 21,052,056 – 21,052,176
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.95
Mean single sequence MFE -26.70
Consensus MFE -19.91
Energy contribution -20.63
Covariance contribution 0.72
Combinations/Pair 1.12
Mean z-score -1.71
Structure conservation index 0.75
SVM decision value 0.12
SVM RNA-class probability 0.595490
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21052056 120 - 23771897
UAAAACACGAAACUUUUGCAUUUAAUUGGGCAAAUUUGCGCGAGUCAAGCAAGGGAUAUGAGCAAAGUUGAGGUGCAACAAAGUGUUUUUAUUCAGCUUUGAAGCGAGUGAGAAGAAAAG
.....(((....(((((((......(((.(((....))).))).....)))))))...((..((((((((((....(((.....)))....))))))))))...)).))).......... ( -29.10)
>DroSec_CAF1 107205 119 - 1
UAAAACACGAAAAU-UUGCAUUUAAUUGGGCAAGUUUGCGCGAGCCAAGCAAGGGAUAUGAGCAAAGUUAAGGAGCAAAAAAGUGUAUUUAUUCAGCUUUGAAGCGAGUGAGAAGAAAAG
....((((.....(-((((.(((((((..((..((((((....).))))).(......)..))..)))))))..)))))...)))).(((((((.(((....))))))))))........ ( -25.60)
>DroSim_CAF1 13418 119 - 1
UAAAACACGAAAAU-UUGCAUUUAAUUGGGCAAGUUUGCGCGAGUCGAGCAAGGGAUAUGAGCAAAGUUGAGGUGCAAAAAAGUGUAUUUAUUCAGCUUUGAAGCGAGUGAGAAGAAAAG
....((((.....(-((((((((.......(((.(((((.((.(((........))).)).))))).))))))))))))...)))).(((((((.(((....))))))))))........ ( -27.91)
>DroEre_CAF1 29626 118 - 1
UAAAACAUGAAA-U-UUGCAUUUAAUUGAGCAAGUUUGCCCGAGUCAAGCGGGGGAUACGAGAAAAGUUGAGGUGCAACAAAGUGUAUUUAUUCUGCUUUGAAGCGAGUGACAAGAAAAU
....((((....-.-((((((((((((...(..((((.((((.......)))).)).))..)...)))))).))))))....))))..((((((.(((....)))))))))......... ( -25.80)
>DroYak_CAF1 682 118 - 1
UAAAACAAGAAA-U-UUGCAUUUAAUUGGGCAAGUUUGCGCGAGUCAAGCAAGGGAUACGAGAAAAGUUGCGAUGCGACAAAGUGUAUUUAUUCUGCUUUGAAGCGAGUGACAAGAAAAC
........(..(-(-((((.(((((...((((.((((((....).)))))...(((((((......(((((...)))))....)))))))....)))))))))))))))..)........ ( -25.10)
>consensus
UAAAACACGAAA_U_UUGCAUUUAAUUGGGCAAGUUUGCGCGAGUCAAGCAAGGGAUAUGAGCAAAGUUGAGGUGCAACAAAGUGUAUUUAUUCAGCUUUGAAGCGAGUGAGAAGAAAAG
....((((.......((((((((.......(((.(((((.((.(((........))).)).))))).)))))))))))....))))..((((((.(((....)))))))))......... (-19.91 = -20.63 +   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 13:00:35 2006