Locus 2940

Sequence ID 3R_DroMel_CAF1
Location 7,870,430 – 7,870,686
Length 256
Max. P 0.998129
window4730 window4731 window4732 window4733

overview

Window 0

Location 7,870,430 – 7,870,546
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.94
Mean single sequence MFE -41.04
Consensus MFE -37.14
Energy contribution -37.54
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.33
Structure conservation index 0.90
SVM decision value 0.61
SVM RNA-class probability 0.798329
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7870430 116 + 27905053
GUGAGUGUACCACCACUGGCCUGCAAUCAUCCGGACUGGCUCCGGUUGACAUAUGUGGUACUGUGACCGUAUAUGUUCUGCCAUCUGUUAACCCGGAGACGGGCCCAUGAGCCAAA----
((((.(((((((....)))..)))).))))......((((((.(((.((((((((((((......))))))))))))..))).........((((....)))).....))))))..---- ( -41.60)
>DroSec_CAF1 2244 117 + 1
GUGAGUGUACCACCACUGGCCUGCAAUCAUCCGGACUGGCUCCGGUUGACAUAUGUGGUACUGUGACCGUAUAUGUUCUGCCAUCUGUUAGCCCGGAGACGGGCCCAUGAGCCAAAA---
((((.(((((((....)))..)))).))))......((((((.(((.((((((((((((......))))))))))))..)))........(((((....)))))....))))))...--- ( -45.10)
>DroSim_CAF1 2252 117 + 1
GUGAGUGUACCACCACUGGCCUGCAAUCAUCCGGACUGGCUCCGGUUGACAUAUGUGGUACUGUGACCGUAUAUGUUCUGCCAUCUGUUAACCCGGAGACGGGCCCAUGAGCCAAAA---
((((.(((((((....)))..)))).))))......((((((.(((.((((((((((((......))))))))))))..))).........((((....)))).....))))))...--- ( -41.60)
>DroEre_CAF1 2304 116 + 1
GCGAGUGUACCACCACUGGCCUGCAAUCAUCCGGACUGGCUCCGGUUGACAUAUGUGGUACUGUGACCGUAUAUGUUCUGCCAUCUGUUAACCCGGAGACGGGACCAUGAACCAAA----
((.((((......)))).))..(((.(((.(((((.....))))).)))((((((((((......))))))))))...)))..........((((....)))).............---- ( -38.00)
>DroYak_CAF1 2274 120 + 1
GUGAGUGUACCACCACUGGCCUGCAAUCAUCCGGACUGGCUCCGGUUGACAUAUGUGGCACUGUGACCGUAUAUGUUCUGCCAUCUGUUAACCCGGAGACGGGCCCAUGAACGAGAAGGG
(((.(((...)))))).((((((...((.(((((..((((...(((.((((((((((((.....).)))))))))))..)))....))))..)))))))))))))............... ( -38.90)
>consensus
GUGAGUGUACCACCACUGGCCUGCAAUCAUCCGGACUGGCUCCGGUUGACAUAUGUGGUACUGUGACCGUAUAUGUUCUGCCAUCUGUUAACCCGGAGACGGGCCCAUGAGCCAAAA___
...((((......))))((((((...((.(((((..((((...(((.((((((((((((......))))))))))))..)))....))))..)))))))))))))............... (-37.14 = -37.54 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 7,870,470 – 7,870,573
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.40
Mean single sequence MFE -36.70
Consensus MFE -27.86
Energy contribution -28.06
Covariance contribution 0.20
Combinations/Pair 1.08
Mean z-score -1.63
Structure conservation index 0.76
SVM decision value 0.17
SVM RNA-class probability 0.618505
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7870470 103 + 27905053
UCCGGUUGACAUAUGUGGUACUGUGACCGUAUAUGUUCUGCCAUCUGUUAACCCGGAGACGGGCCCAUGAGCCAAA-------AAGGGGACCAAAAGGGAACGGGGCGCA----------
.(((((.((((((((((((......))))))))))))..)))..(((((..((((....))))(((.((..((...-------....))..))...))))))))))....---------- ( -36.10)
>DroSec_CAF1 2284 104 + 1
UCCGGUUGACAUAUGUGGUACUGUGACCGUAUAUGUUCUGCCAUCUGUUAGCCCGGAGACGGGCCCAUGAGCCAAAA------AAGGGGACCAAAAGGGUAAGGGGCGCA----------
...(((.((((((((((((......))))))))))))..)))........(((((....)))((((....(((....------..(....)......)))...)))))).---------- ( -38.20)
>DroSim_CAF1 2292 104 + 1
UCCGGUUGACAUAUGUGGUACUGUGACCGUAUAUGUUCUGCCAUCUGUUAACCCGGAGACGGGCCCAUGAGCCAAAA------AAGGGGACCAAAAGGGUAAGGGGCGCA----------
...(((.((((((((((((......))))))))))))..)))..........(((....)))((((....(((....------..(....)......)))...))))...---------- ( -36.40)
>DroEre_CAF1 2344 112 + 1
UCCGGUUGACAUAUGUGGUACUGUGACCGUAUAUGUUCUGCCAUCUGUUAACCCGGAGACGGGACCAUGAACCAAA--------AAAGGGCUAAAAGGGAACUGGGUGCAGAGGUUCGGA
(((((..((((((((((((......))))))))))))..(((.(((((...((((....))))(((.....((...--------...))......((....)).)))))))))))))))) ( -39.40)
>DroYak_CAF1 2314 110 + 1
UCCGGUUGACAUAUGUGGCACUGUGACCGUAUAUGUUCUGCCAUCUGUUAACCCGGAGACGGGCCCAUGAACGAGAAGGGGGUAAAGGGGCUAAAAGGAAGCGGGGCGCA----------
((((((.((((((((((((.....).)))))))))))..))).(((.((..((((....))))(((...........)))....)).)))......))).(((...))).---------- ( -33.40)
>consensus
UCCGGUUGACAUAUGUGGUACUGUGACCGUAUAUGUUCUGCCAUCUGUUAACCCGGAGACGGGCCCAUGAGCCAAAA______AAGGGGACCAAAAGGGAACGGGGCGCA__________
...(((.((((((((((((......))))))))))))..)))..........(((....)))((((.....((..............)).((....)).....))))............. (-27.86 = -28.06 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 7,870,573 – 7,870,686
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.73
Mean single sequence MFE -29.06
Consensus MFE -27.54
Energy contribution -27.58
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.71
Structure conservation index 0.95
SVM decision value 2.17
SVM RNA-class probability 0.989449
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7870573 113 + 27905053
------GAGGUUCAGCUGUCACUCAGAUCUCUCCGCUUUGGUUUAACAUUUCCCUUU-UUUAGCUUAUCCCAGUGACCUCACUGUGGGGAUUUUGCUUUUUGGGGAUUUUAUUGACUCUG
------(((((....(((.....))))))))........((((.......(((((..-...(((..(((((((((....))))...)))))...)))....))))).......))))... ( -28.54)
>DroSec_CAF1 2388 114 + 1
------GAGGUUCAGCUGUCACUCAGAUCUCUCCGCUUUGGUUUAACAUUUCCCUUUUUUUAGCUUGUCCCAGUGACCUCACUGUGGGGAUUUUGCUUUUUGGGGAUUUUAUUGACUCUG
------(((((....(((.....))))))))........((((.......(((((......(((..(((((((((....))))...)))))...)))....))))).......))))... ( -28.24)
>DroSim_CAF1 2396 114 + 1
------GAGGUUCAGCUGUCACUCAGAUCUCUCCGCUUUGGUUUAACAUUUCCCUUUUUUUAGCUUAUCCCAGUGACCUCACUGUGGGGAUUUUGCUUUUUGGGGAUUUUAUUGACUCUG
------(((((....(((.....))))))))........((((.......(((((......(((..(((((((((....))))...)))))...)))....))))).......))))... ( -27.94)
>DroEre_CAF1 2456 119 + 1
GGCUCAGAGGUUCAGCUGUCACUCAGAUCUCUCCGCUUUGGUUUAACAUUUCCCAUU-UUUAGCUUAUCCCAGUGACCUCACUGUGGGGAUUUUGCUUUUUGGGGAUUUUAUUGACUCUG
(((..((((((....(((.....)))))))))..)))..((((......((((((..-...(((..(((((((((....))))...)))))...)))...)))))).......))))... ( -32.02)
>DroYak_CAF1 2424 113 + 1
------GAGGUUCAGCUGUCACUCAGAUCUCUCCGCUUUGGUUUAACAUUUCCCUUU-UUUAGCUUAUCCCAGUGACCUCACUGUGGGGAUUUUGCUUUUUGGGGAUUUUAUUGACUCUG
------(((((....(((.....))))))))........((((.......(((((..-...(((..(((((((((....))))...)))))...)))....))))).......))))... ( -28.54)
>consensus
______GAGGUUCAGCUGUCACUCAGAUCUCUCCGCUUUGGUUUAACAUUUCCCUUU_UUUAGCUUAUCCCAGUGACCUCACUGUGGGGAUUUUGCUUUUUGGGGAUUUUAUUGACUCUG
......(((((....(((.....))))))))........((((.......(((((......(((..(((((((((....))))...)))))...)))....))))).......))))... (-27.54 = -27.58 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 7,870,573 – 7,870,686
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.73
Mean single sequence MFE -26.14
Consensus MFE -25.04
Energy contribution -25.24
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.96
Structure conservation index 0.96
SVM decision value 3.01
SVM RNA-class probability 0.998129
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7870573 113 - 27905053
CAGAGUCAAUAAAAUCCCCAAAAAGCAAAAUCCCCACAGUGAGGUCACUGGGAUAAGCUAAA-AAAGGGAAAUGUUAAACCAAAGCGGAGAGAUCUGAGUGACAGCUGAACCUC------
(((.((((......((((.....(((...(((((...((((....)))))))))..)))...-...))))...............((((....))))..))))..)))......------ ( -26.10)
>DroSec_CAF1 2388 114 - 1
CAGAGUCAAUAAAAUCCCCAAAAAGCAAAAUCCCCACAGUGAGGUCACUGGGACAAGCUAAAAAAAGGGAAAUGUUAAACCAAAGCGGAGAGAUCUGAGUGACAGCUGAACCUC------
(((.((((......((((.....(((....((((...((((....))))))))...))).......))))...............((((....))))..))))..)))......------ ( -24.00)
>DroSim_CAF1 2396 114 - 1
CAGAGUCAAUAAAAUCCCCAAAAAGCAAAAUCCCCACAGUGAGGUCACUGGGAUAAGCUAAAAAAAGGGAAAUGUUAAACCAAAGCGGAGAGAUCUGAGUGACAGCUGAACCUC------
(((.((((......((((.....(((...(((((...((((....)))))))))..))).......))))...............((((....))))..))))..)))......------ ( -25.50)
>DroEre_CAF1 2456 119 - 1
CAGAGUCAAUAAAAUCCCCAAAAAGCAAAAUCCCCACAGUGAGGUCACUGGGAUAAGCUAAA-AAUGGGAAAUGUUAAACCAAAGCGGAGAGAUCUGAGUGACAGCUGAACCUCUGAGCC
((((((((......((((.....(((...(((((...((((....)))))))))..)))...-...))))..(((((........((((....))))..)))))..)))..))))).... ( -29.00)
>DroYak_CAF1 2424 113 - 1
CAGAGUCAAUAAAAUCCCCAAAAAGCAAAAUCCCCACAGUGAGGUCACUGGGAUAAGCUAAA-AAAGGGAAAUGUUAAACCAAAGCGGAGAGAUCUGAGUGACAGCUGAACCUC------
(((.((((......((((.....(((...(((((...((((....)))))))))..)))...-...))))...............((((....))))..))))..)))......------ ( -26.10)
>consensus
CAGAGUCAAUAAAAUCCCCAAAAAGCAAAAUCCCCACAGUGAGGUCACUGGGAUAAGCUAAA_AAAGGGAAAUGUUAAACCAAAGCGGAGAGAUCUGAGUGACAGCUGAACCUC______
(((.((((......((((.....(((...(((((...((((....)))))))))..))).......))))...............((((....))))..))))..)))............ (-25.04 = -25.24 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:18 2006