Locus 2688

Sequence ID 3R_DroMel_CAF1
Location 7,224,776 – 7,224,917
Length 141
Max. P 0.992772
window4363 window4364 window4365

overview

Window 3

Location 7,224,776 – 7,224,880
Length 104
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 75.97
Mean single sequence MFE -33.03
Consensus MFE -18.43
Energy contribution -18.13
Covariance contribution -0.30
Combinations/Pair 1.22
Mean z-score -2.78
Structure conservation index 0.56
SVM decision value 2.35
SVM RNA-class probability 0.992772
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7224776 104 + 27905053
-GA--C--GGGGGUCGG--ACAUGGCCCCCAGACAAUAGCCCAGCAAUAUUAUUAUUAUUU-CCCAAUCGGCGU--CCUUUGUAAUCCUUCGAGGAUUAAAGGUGCGCCACCAG---
-..--.--((((((((.--...))))))))...............................-.......(((((--((((..((((((.....)))))))))).))))).....--- ( -34.80)
>DroVir_CAF1 68802 107 + 1
AAA--U--GUGCGCCUC--AAC-GAGCCACAGACAAUAGCCCAGCAAUAUUAUUCUUAUUUUCCCAAUGGGCGCCAUCUUUGUAAUUCCCCGAGAAUUAAAGUGGCGCCAA---CCA
...--(--(((.((...--...-..))))))......................................(((((((.(((..((((((.....))))))))))))))))..---... ( -24.50)
>DroPse_CAF1 91793 107 + 1
AAA--UGAAGGGGCGGG--AGGU--GCCCCAGACAAUAGCCCAGUAAUAUUAUUAUUAUUU-CCAAUAGGGCGC-AUCUUUGUAAUCCCCCGAGGAUUAAAGAUGCGCCAAAAG--A
...--....((((((..--...)--)))))............(((((((....))))))).-.......(((((-(((((..((((((.....)))))))))))))))).....--. ( -36.70)
>DroGri_CAF1 92190 106 + 1
-AU--U--GUGCGCCUC--AGA-GUGCCACAGACAAUAGCCCAGAAAUAUUAUUCUUAUUUUCCCA--GGGCGCCUUCUUUGUAAUUCCUCGAGGAUUAAAGAGGCGCCAAAAACC-
-.(--(--(.(((((((--((.-(((((...((.((((....((((......)))))))).))...--.)))))))((((((........)))))).....)))))))))).....- ( -31.60)
>DroAna_CAF1 55870 108 + 1
-GAACC--GGGGGCACCACAGACAACCCCCAGACAAUAGCCCAGCAAUAUUAUUAUUAUUU-CCCACUGGGCGC--CCUUUGUAAUCCUUCGAGGAUUAAAGGCGCGCCACCAG---
-.....--(((((............)))))........((((((.................-....))))))((--((((..((((((.....)))))))))).))........--- ( -32.00)
>DroPer_CAF1 94872 107 + 1
AAA--UGAAGGGGCGGG--AGGU--GCCCCAGACAAUAGCCCAGUAAUAUUAUUAUUAUUU-CCAAUUGGGCGC-AUCUUUGUAAUCCCCCGAGGAUUAAAGAUGCGCCAAAAG--A
...--....((((((..--...)--)))))...((((.(...(((((((....))))))).-.).))))(((((-(((((..((((((.....)))))))))))))))).....--. ( -38.60)
>consensus
_AA__U__GGGGGCCGC__AGAUG_GCCCCAGACAAUAGCCCAGCAAUAUUAUUAUUAUUU_CCCAAUGGGCGC_AUCUUUGUAAUCCCCCGAGGAUUAAAGAUGCGCCAAAAG___
..........((((........................))))...........................(((((...(((..((((((.....)))))))))..)))))........ (-18.43 = -18.13 +  -0.30)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 7,224,776 – 7,224,880
Length 104
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 75.97
Mean single sequence MFE -35.31
Consensus MFE -18.48
Energy contribution -18.26
Covariance contribution -0.22
Combinations/Pair 1.14
Mean z-score -2.41
Structure conservation index 0.52
SVM decision value 1.69
SVM RNA-class probability 0.972278
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7224776 104 - 27905053
---CUGGUGGCGCACCUUUAAUCCUCGAAGGAUUACAAAGG--ACGCCGAUUGGG-AAAUAAUAAUAAUAUUGCUGGGCUAUUGUCUGGGGGCCAUGU--CCGACCCCC--G--UC-
---(..((((((..((((((((((.....))))))..))))--.)))).))..).-...................((((....))))(((((.(....--..).)))))--.--..- ( -32.60)
>DroVir_CAF1 68802 107 - 1
UGG---UUGGCGCCACUUUAAUUCUCGGGGAAUUACAAAGAUGGCGCCCAUUGGGAAAAUAAGAAUAAUAUUGCUGGGCUAUUGUCUGUGGCUC-GUU--GAGGCGCAC--A--UUU
.((---(.((((((((((((((((.....))))))..))).))))))).)))...................(((.(((((((.....)))))))-((.--...))))).--.--... ( -30.00)
>DroPse_CAF1 91793 107 - 1
U--CUUUUGGCGCAUCUUUAAUCCUCGGGGGAUUACAAAGAU-GCGCCCUAUUGG-AAAUAAUAAUAAUAUUACUGGGCUAUUGUCUGGGGC--ACCU--CCCGCCCCUUCA--UUU
.--.....((((((((((((((((.....))))))..)))))-)))))....(((-(..................((((....))))(((((--....--...)))))))))--... ( -37.30)
>DroGri_CAF1 92190 106 - 1
-GGUUUUUGGCGCCUCUUUAAUCCUCGAGGAAUUACAAAGAAGGCGCCC--UGGGAAAAUAAGAAUAAUAUUUCUGGGCUAUUGUCUGUGGCAC-UCU--GAGGCGCAC--A--AU-
-.....((((((((((.....(((....)))....((.(((....((((--.(((((.((.......)).))))))))).....))).))....-...--))))))).)--)--).- ( -30.40)
>DroAna_CAF1 55870 108 - 1
---CUGGUGGCGCGCCUUUAAUCCUCGAAGGAUUACAAAGG--GCGCCCAGUGGG-AAAUAAUAAUAAUAUUGCUGGGCUAUUGUCUGGGGGUUGUCUGUGGUGCCCCC--GGUUC-
---..(((((((((((((((((((.....))))))...)))--))))((((..(.-..............)..))))))))))..((((((((..........))))))--))...- ( -44.26)
>DroPer_CAF1 94872 107 - 1
U--CUUUUGGCGCAUCUUUAAUCCUCGGGGGAUUACAAAGAU-GCGCCCAAUUGG-AAAUAAUAAUAAUAUUACUGGGCUAUUGUCUGGGGC--ACCU--CCCGCCCCUUCA--UUU
.--.....((((((((((((((((.....))))))..)))))-)))))....(((-(..................((((....))))(((((--....--...)))))))))--... ( -37.30)
>consensus
___CUUUUGGCGCAUCUUUAAUCCUCGAGGGAUUACAAAGAU_GCGCCCAAUGGG_AAAUAAUAAUAAUAUUGCUGGGCUAUUGUCUGGGGC_CAUCU__CCGGCCCCC__A__UU_
........(((((..(((((((((.....))))))..)))...)))))...........................((((....))))((((..............))))........ (-18.48 = -18.26 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 7,224,809 – 7,224,917
Length 108
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 78.26
Mean single sequence MFE -22.57
Consensus MFE -13.27
Energy contribution -12.50
Covariance contribution -0.77
Combinations/Pair 1.44
Mean z-score -2.19
Structure conservation index 0.59
SVM decision value 1.15
SVM RNA-class probability 0.922797
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7224809 108 + 27905053
CCAGCAAUAUUAUUAUUAUUU-CCCAAUCG-GCGU--CCUUUGUAAUCCUUCGAGGAUUAAAGGUGCGCCACCAG----CCGUCGUCAACUGAAGUACAACCAAAACGA-AAUCGCA
...((((((....))))((((-(......(-((((--((((..((((((.....)))))))))).))))).....----..(((.((....)).).)).........))-))).)). ( -22.80)
>DroVir_CAF1 68835 111 + 1
CCAGCAAUAUUAUUCUUAUUUUCCCAAUGG-GCGCCAUCUUUGUAAUUCCCCGAGAAUUAAAGUGGCGCCAA---CCAACCGUA-AAAACAGAAGUACAACCAAACCAA-AAACAAA
............((((.............(-((((((.(((..((((((.....))))))))))))))))..---......((.-...))))))...............-....... ( -19.60)
>DroPse_CAF1 91827 110 + 1
CCAGUAAUAUUAUUAUUAUUU-CCAAUAGG-GCGC-AUCUUUGUAAUCCCCCGAGGAUUAAAGAUGCGCCAAAAG--AACCGUCAACAACAGAAGUACAACCAA-AAUG-AAACGCA
................(((((-(......(-((((-(((((..((((((.....))))))))))))))))....(--(....)).......)))))).......-....-....... ( -25.60)
>DroGri_CAF1 92222 109 + 1
CCAGAAAUAUUAUUCUUAUUUUCCCA--GG-GCGCCUUCUUUGUAAUUCCUCGAGGAUUAAAGAGGCGCCAAAAACC-GCCGUA--AAACAGAAGUACAACCAAAC-AA-AAACAAA
...((((((.......))))))....--.(-((((((.(((((....(((....))).)))))))))))).......-......--....................-..-....... ( -22.20)
>DroWil_CAF1 84950 107 + 1
CCAGUAAUAUUUUUAUUAUUU-CACAAUUGUGUGC-AUCUUUGUAAUUCUUCGAGAAUUAAAGAUGUGCCG--AU----CCGUA--AAACUGAAGUACAACCAAUAUAAGAAACAAA
.((((((((....))))....-.((.((((.(..(-(((((..((((((.....))))))))))))..)))--))----..)).--..))))......................... ( -18.80)
>DroPer_CAF1 94906 111 + 1
CCAGUAAUAUUAUUAUUAUUU-CCAAUUGG-GCGC-AUCUUUGUAAUCCCCCGAGGAUUAAAGAUGCGCCAAAAG--AACCGUCAACAACAGAAGUACAACCAAAAAUG-AAACGCA
................(((((-(...((((-((((-(((((..((((((.....))))))))))))))))....(--(....))..)))..))))))............-....... ( -26.40)
>consensus
CCAGUAAUAUUAUUAUUAUUU_CCCAAUGG_GCGC_AUCUUUGUAAUCCCCCGAGGAUUAAAGAUGCGCCAAAAG___ACCGUA_AAAACAGAAGUACAACCAAAAAAA_AAACAAA
.............................(.((((.(((((..((((((.....))))))))))))))))............................................... (-13.27 = -12.50 +  -0.77)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:17 2006