Locus 6583

Sequence ID	3R_DroMel_CAF1
Location	17,333,527 – 17,333,815
Length	288
Max. P	0.999395

overview

Window 2

Location	17,333,527 – 17,333,634
Length	107
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.96
Mean single sequence MFE	-29.82
Consensus MFE	-16.55
Energy contribution	-16.22
Covariance contribution	-0.33
Combinations/Pair	1.43
Mean z-score	-2.12
Structure conservation index	0.55
SVM decision value	0.91
SVM RNA-class probability	0.880669
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17333527 107 + 27905053
---UU-------ACACGGCUAAUGCCCAGUA---CGGUGUAACUCAACUAGAUUAUAGGGCAUCAAAGCCCGACGCGCAUAAACGGGGAGCAAAUGGCUUAUACAAUAUGCAUGAGCACA
---((-------(((((((....)))(....---.)))))))((((...........((((......)))).....(((((......((((.....))))......))))).)))).... ( -28.50)
>DroPse_CAF1 16940 118 + 1
AGAUGAGGUCUUGCAAA--CAAUGUUUUAUUUGUGGGUAUACCCCAACUAGAAAAGAGGAAUACAAAGCGUGAUGUACACGAGCGGGGAGUAAAUGGCUCAUUCAAUAUGCAUGAGCACA
........((((((...--.....(((((.(((.(((....)))))).)))))...............((((.....)))).))))))........((((((.(.....).))))))... ( -26.40)
>DroSec_CAF1 9495 107 + 1
---UU-------ACAUGACUAAAAUCAUGUU---CGUUGUAACCCAACUAGAUUAUAGGGCAUCAAAGCCCGACGCGCAUAAACGGGGAGCAAAUGGCUCAUACAAUAUGCAUGAGCACA
---..-------............((((((.---.((((((.(((............((((......)))).............)))((((.....)))).))))))..))))))..... ( -29.81)
>DroSim_CAF1 15119 107 + 1
---UU-------ACACGACUAAAAUCAUGUU---CGUUGUAACCCAACUAGAUUAUAGGGCAUCAAAGCCCGACGCGCAUAAACGGGGAGCAAAUAGCUCAUACAAUAUGCAUGAGCACA
---..-------............((((((.---.((((((.(((............((((......)))).............)))((((.....)))).))))))..))))))..... ( -29.91)
>DroEre_CAF1 14706 106 + 1
---UU-------GCAAGGCUAGUGCCUAGUU---UCGCAUA-CCCAACUAGACCAUAGGGCAUCAAAGCCCGGCGCGCAUAAACGGGGAGCAAAUGGCUCAUACAAUAUGCAUGAGCACA
---..-------.....(((.((((((((((---.......-...))))).......((((......)))))))))(((((......((((.....))))......)))))...)))... ( -32.40)
>DroYak_CAF1 13043 107 + 1
---UC-------ACCAGGCUAAUGCCUAGUC---CCGUAUAACCCAACUAGACCAUAGGGCAUCAAAGCCCGACGCGCAUAAACGGCGAGCAAAUGGCUCAUACAAUAUGCAUGGGCACA
---..-------...((((....)))).(((---((((...................((((......)))).....(((((......((((.....))))......)))))))))).)). ( -31.90)
>consensus
___UU_______ACAAGGCUAAUGCCUAGUU___CGGUAUAACCCAACUAGAUUAUAGGGCAUCAAAGCCCGACGCGCAUAAACGGGGAGCAAAUGGCUCAUACAAUAUGCAUGAGCACA
............((.(((......))).))............(((............((((......))))..((........)))))........((((((.(.....).))))))... (-16.55 = -16.22 +  -0.33)

alignment

secondary structure

dotplot

Window 3

Location	17,333,527 – 17,333,634
Length	107
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.96
Mean single sequence MFE	-31.77
Consensus MFE	-24.39
Energy contribution	-23.57
Covariance contribution	-0.83
Combinations/Pair	1.54
Mean z-score	-1.69
Structure conservation index	0.77
SVM decision value	1.19
SVM RNA-class probability	0.928551
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17333527 107 - 27905053
UGUGCUCAUGCAUAUUGUAUAAGCCAUUUGCUCCCCGUUUAUGCGCGUCGGGCUUUGAUGCCCUAUAAUCUAGUUGAGUUACACCG---UACUGGGCAUUAGCCGUGU-------AA---
((((((((.....((((((...(((((..((.....))..))).))...((((......)))))))))).....)))).))))...---(((..(((....)))..))-------).--- ( -27.40)
>DroPse_CAF1 16940 118 - 1
UGUGCUCAUGCAUAUUGAAUGAGCCAUUUACUCCCCGCUCGUGUACAUCACGCUUUGUAUUCCUCUUUUCUAGUUGGGGUAUACCCACAAAUAAAACAUUG--UUUGCAAGACCUCAUCU
(((((....)))))....((((((............))))))(((((........)))))...........((.((((((.......(((((((....)))--))))....)))))).)) ( -22.30)
>DroSec_CAF1 9495 107 - 1
UGUGCUCAUGCAUAUUGUAUGAGCCAUUUGCUCCCCGUUUAUGCGCGUCGGGCUUUGAUGCCCUAUAAUCUAGUUGGGUUACAACG---AACAUGAUUUUAGUCAUGU-------AA---
((.((((((((.....)))))))))).(((..((((((....)))....((((......))))............)))...)))..---.(((((((....)))))))-------..--- ( -32.60)
>DroSim_CAF1 15119 107 - 1
UGUGCUCAUGCAUAUUGUAUGAGCUAUUUGCUCCCCGUUUAUGCGCGUCGGGCUUUGAUGCCCUAUAAUCUAGUUGGGUUACAACG---AACAUGAUUUUAGUCGUGU-------AA---
...((((((((.....)))))))).................((((((.(((((......))))((.((((..((((.....)))).---.....)))).))).)))))-------).--- ( -32.60)
>DroEre_CAF1 14706 106 - 1
UGUGCUCAUGCAUAUUGUAUGAGCCAUUUGCUCCCCGUUUAUGCGCGCCGGGCUUUGAUGCCCUAUGGUCUAGUUGGG-UAUGCGA---AACUAGGCACUAGCCUUGC-------AA---
((.((((((((.....))))))))))(((((..((((.(((.((.((..((((......))))..)))).))).))))-...))))---)...((((....))))...-------..--- ( -37.70)
>DroYak_CAF1 13043 107 - 1
UGUGCCCAUGCAUAUUGUAUGAGCCAUUUGCUCGCCGUUUAUGCGCGUCGGGCUUUGAUGCCCUAUGGUCUAGUUGGGUUAUACGG---GACUAGGCAUUAGCCUGGU-------GA---
...(((((.(((((.....(((((.....))))).....))))).(((.((((......)))).))).......))))).......---.(((((((....)))))))-------..--- ( -38.00)
>consensus
UGUGCUCAUGCAUAUUGUAUGAGCCAUUUGCUCCCCGUUUAUGCGCGUCGGGCUUUGAUGCCCUAUAAUCUAGUUGGGUUACACCG___AACAAGACAUUAGCCUUGU_______AA___
((((((((((((((......((((.....))))......))))))....((((......))))...........)))).))))........((((((....))))))............. (-24.39 = -23.57 +  -0.83)

alignment

secondary structure

dotplot

Window 4

Location	17,333,554 – 17,333,672
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	74.87
Mean single sequence MFE	-30.28
Consensus MFE	-15.48
Energy contribution	-15.12
Covariance contribution	-0.36
Combinations/Pair	1.26
Mean z-score	-2.20
Structure conservation index	0.51
SVM decision value	1.62
SVM RNA-class probability	0.968094
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17333554 118 + 27905053
AACUCAACUAGAUUAUAGGGCAUCAAAGCCCGACGCGCAUAAACGGGGAGCAAAUGGCUUAUACAAUAUGCAUGAGCACAUUAAAUGAACAGCACC--CAGCCCCAAGAAAAAGGGGAGC
.................((((......)))).....((.......(((.((.....((((((.(.....).)))))).(((...)))....)).))--)..((((........)))).)) ( -29.00)
>DroPse_CAF1 16978 116 + 1
ACCCCAACUAGAAAAGAGGAAUACAAAGCGUGAUGUACACGAGCGGGGAGUAAAUGGCUCAUUCAAUAUGCAUGAGCACAUUAAAUGAAAAACUCG--CAGCUCCAAUG--AUGGGGAGC
.(((((.......................(((.....)))((((.(.((((.((((((((((.(.....).)))))).))))...(....))))).--).)))).....--.)))))... ( -32.50)
>DroSec_CAF1 9522 118 + 1
AACCCAACUAGAUUAUAGGGCAUCAAAGCCCGACGCGCAUAAACGGGGAGCAAAUGGCUCAUACAAUAUGCAUGAGCACAUUAAAUGAACAGCGCC--CAGCCCCAAGAAAAAGGGGAGC
.................((((......))))...((((.......(....).((((((((((.(.....).)))))).)))).........)))).--...((((........))))... ( -32.00)
>DroAna_CAF1 13612 107 + 1
ACCCCAACUAGACUGAAGUUU------------CUGGCUUAAACAGGGAGUAAAUGGCUUAUAAAAAAUUCAUGAGAACAUUAAAUGAGCAGCACUCGCAGCCCCAAA-GACAGGGGAGC
.((((..(((((........)------------))))........(((.((.....((((((......(((....)))......)))))).((....)).)))))...-....))))... ( -25.20)
>DroPer_CAF1 17984 116 + 1
ACCCCAAGUAGAAAAGAGGAAUACAAAGCGUGAUGUAUACGAGCGGGGAGUAAAUGGCUCAUUCAAUAUGCAUGAGCACAUUAAAUGAAAAACUCG--CAGCUCCAAUG--AUGGGGAGC
.(((((............(.(((((........))))).)((((.(.((((.((((((((((.(.....).)))))).))))...(....))))).--).)))).....--.)))))... ( -32.70)
>consensus
ACCCCAACUAGAAUAGAGGAAAACAAAGCCCGACGCGCAUAAACGGGGAGUAAAUGGCUCAUACAAUAUGCAUGAGCACAUUAAAUGAACAGCACC__CAGCCCCAAGA_AAAGGGGAGC
.((((......................((.....)).........(((.((.((((((((((.(.....).)))))).))))....(.....).......)))))........))))... (-15.48 = -15.12 +  -0.36)

alignment

secondary structure

dotplot

Window 5

Location	17,333,554 – 17,333,672
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	74.87
Mean single sequence MFE	-35.02
Consensus MFE	-18.06
Energy contribution	-17.06
Covariance contribution	-1.00
Combinations/Pair	1.38
Mean z-score	-2.96
Structure conservation index	0.52
SVM decision value	3.57
SVM RNA-class probability	0.999395
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17333554 118 - 27905053
GCUCCCCUUUUUCUUGGGGCUG--GGUGCUGUUCAUUUAAUGUGCUCAUGCAUAUUGUAUAAGCCAUUUGCUCCCCGUUUAUGCGCGUCGGGCUUUGAUGCCCUAUAAUCUAGUUGAGUU
(((((((........)))((((--(((((.........(((((((....)))))))((((((((............))))))))))...((((......))))....))))))).)))). ( -36.50)
>DroPse_CAF1 16978 116 - 1
GCUCCCCAU--CAUUGGAGCUG--CGAGUUUUUCAUUUAAUGUGCUCAUGCAUAUUGAAUGAGCCAUUUACUCCCCGCUCGUGUACAUCACGCUUUGUAUUCCUCUUUUCUAGUUGGGGU
...(((((.--(....((((.(--.((((..((((((((((((((....))))))))))))))......)))).).))))(.(((((........))))).)..........).))))). ( -37.60)
>DroSec_CAF1 9522 118 - 1
GCUCCCCUUUUUCUUGGGGCUG--GGCGCUGUUCAUUUAAUGUGCUCAUGCAUAUUGUAUGAGCCAUUUGCUCCCCGUUUAUGCGCGUCGGGCUUUGAUGCCCUAUAAUCUAGUUGGGUU
(((((((........)))((((--(((((.((((((.((((((((....)))))))).))))))(((..((.....))..))).)))))((((......)))).......)))).)))). ( -40.60)
>DroAna_CAF1 13612 107 - 1
GCUCCCCUGUC-UUUGGGGCUGCGAGUGCUGCUCAUUUAAUGUUCUCAUGAAUUUUUUAUAAGCCAUUUACUCCCUGUUUAAGCCAG------------AAACUUCAGUCUAGUUGGGGU
...((((...(-(...((((((.(((((..(((.((..((.((((....)))).))..)).)))....))))).(((.......)))------------......))))))))..)))). ( -23.70)
>DroPer_CAF1 17984 116 - 1
GCUCCCCAU--CAUUGGAGCUG--CGAGUUUUUCAUUUAAUGUGCUCAUGCAUAUUGAAUGAGCCAUUUACUCCCCGCUCGUAUACAUCACGCUUUGUAUUCCUCUUUUCUACUUGGGGU
...(((((.--.....((((.(--.((((..((((((((((((((....))))))))))))))......)))).).))))(.(((((........))))).)............))))). ( -36.70)
>consensus
GCUCCCCUUU_CAUUGGGGCUG__CGAGCUGUUCAUUUAAUGUGCUCAUGCAUAUUGUAUGAGCCAUUUACUCCCCGUUUAUGCACGUCACGCUUUGAAGCCCUAUAAUCUAGUUGGGGU
(((((..........)))))...........((((...(((((((....)))))))((((((((............))))))))..............................)))).. (-18.06 = -17.06 +  -1.00)

alignment

secondary structure

dotplot

Window 6

Location	17,333,594 – 17,333,699
Length	105
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	88.39
Mean single sequence MFE	-29.47
Consensus MFE	-23.39
Energy contribution	-23.37
Covariance contribution	-0.02
Combinations/Pair	1.21
Mean z-score	-2.91
Structure conservation index	0.79
SVM decision value	0.78
SVM RNA-class probability	0.848520
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17333594 105 - 27905053
ACCCCUCUC-CGUAAGCCUCGUAAAUAUGCUCCCCUUUUUCUUGGGGCUG--GGUGCUGUUCAUUUAAUGUGCUCAUGCAUAUUGUAUAAGCCAUUUGCUCCCCGUUU
.........-....(((((((..((.............))..)))))))(--((.((.(((.((.((((((((....)))))))).)).))).....)).)))..... ( -24.22)
>DroSec_CAF1 9562 103 - 1
CCCC--CUC-CGCAUGCCUCGUAAAUAUGCUCCCCUUUUUCUUGGGGCUG--GGCGCUGUUCAUUUAAUGUGCUCAUGCAUAUUGUAUGAGCCAUUUGCUCCCCGUUU
....--...-.(((((.(((((((((((((.((((........)))).((--(((((............))))))).))))))).)))))).))..)))......... ( -32.40)
>DroSim_CAF1 15186 103 - 1
CCCC--CUC-CGCAUGCCUCGUAAAUAUGCUCCCCUUUUUCUUGGGGCUG--GGCGCUGUUCAUUUAAUGUGCUCAUGCAUAUUGUAUGAGCUAUUUGCUCCCCGUUU
....--...-.(((((.........))))).((((........))))..(--((.((.((((((.((((((((....)))))))).)))))).....)).)))..... ( -32.10)
>DroEre_CAF1 14772 101 - 1
-CCC--CUC-CGUGAGCCUCGUAAAUAUGCUCCCCUUUUUCUUGGGGCUG---GUGCUGUUCAUUUAAUGUGCUCAUGCAUAUUGUAUGAGCCAUUUGCUCCCCGUUU
-...--...-...((((...........))))...........(((((..---(((..((((((.((((((((....)))))))).)))))))))..)))))...... ( -28.80)
>DroYak_CAF1 13110 102 - 1
-UCC--CUC-CGCAAGCCUCGUAAAUAUGCUCCCCUUUUCCUUGGGGCUG--GGUGCUGUUCAUUUAAUGUGCCCAUGCAUAUUGUAUGAGCCAUUUGCUCGCCGUUU
-...--...-.(((((.(((((((((((((.((((........)))).((--((..(............)..)))).))))))).))))))...)))))......... ( -33.20)
>DroAna_CAF1 13640 104 - 1
-CCC--CUCAGGUAAGCCCCAUAAAUACGCUCCCCUGUC-UUUGGGGCUGCGAGUGCUGCUCAUUUAAUGUUCUCAUGAAUUUUUUAUAAGCCAUUUACUCCCUGUUU
-...--..((((..(((((((.....(((......))).-..)))))))..(((((..(((.((..((.((((....)))).))..)).)))....)))))))))... ( -26.10)
>consensus
_CCC__CUC_CGCAAGCCUCGUAAAUAUGCUCCCCUUUUUCUUGGGGCUG__GGUGCUGUUCAUUUAAUGUGCUCAUGCAUAUUGUAUGAGCCAUUUGCUCCCCGUUU
....................((((((.((((((((........)))).....))))..((((((.((((((((....)))))))).)))))).))))))......... (-23.39 = -23.37 +  -0.02)

alignment

secondary structure

dotplot

Window 7

Location	17,333,699 – 17,333,815
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.43
Mean single sequence MFE	-28.45
Consensus MFE	-16.40
Energy contribution	-16.85
Covariance contribution	0.45
Combinations/Pair	1.21
Mean z-score	-1.88
Structure conservation index	0.58
SVM decision value	0.56
SVM RNA-class probability	0.783005
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17333699 116 - 27905053
UGCCUUAAUGCGACUCUAAGCCAUAUAGUUAGCCAGGCAUUGCAACUGCCAUAAAAAACUUGGCAAUUAGCUUGUUUAACAAGAGCG-CUCUUUGUGGCUACAAAAUGCAGC-UACCU--
........((((......(((((((..(((((.(((((........(((((.........)))))....))))).)))))((((...-.)))))))))))......))))..-.....-- ( -27.50)
>DroSec_CAF1 9665 116 - 1
UGUCCUAAUACGACUCUAAGCCAUAUAGUUAGCCAGGCAUUGCAACUGCCAUAAAAAACUUGGCAAUUAGCUUGUUUAACAAGAGCG-CUCUUUGUGGCUACAAAAUGCAGC-UACCU--
.(((.......)))....(((((((..(((((.(((((........(((((.........)))))....))))).)))))((((...-.)))))))))))............-.....-- ( -25.40)
>DroSim_CAF1 15289 116 - 1
UGUCCUAAUGCGACUCUAAGCCAUAUAGUUAGCCAGGCAUUGCAACUGCCAUAAAAAACUUGGCAAUUAGCUUGUUUAACAAGAGCG-CUCUUUGUGGCUACAAAAUGCAGC-CACCU--
.........(((.((((..(((.............)))...((((.(((((.........))))).)).))..........))))))-).....((((((.(.....).)))-)))..-- ( -29.12)
>DroEre_CAF1 14873 102 - 1
UACCUUAAUGCGACUUUAAGCCAUAGAGUUAGCCAGU------------CAUAAAAAACUUGGCAAUUAGCUUGUUUAACAAGAGCU-CUCUUUGUGGCUACAAAAUGCAGCUCC-----
........((((......((((((((((..(((..((------------((.........))))......((((.....)))).)))-..))))))))))......)))).....----- ( -27.20)
>DroYak_CAF1 13212 113 - 1
UACCUCAAUGGUACAUUGAGCCAUAUAGUUAGCCAGGCAUUGCGACUGGCAUAAAAAACUUGGCAAUUAGCUUGUUAAACAAGAGCG-CUCUUUGUGGCUACAAAAUGCAGC-CA-----
.(((.....)))(((..((((....(((((.((((((...(((.....))).......)))))))))))((((.........)))))-)))..)))((((.(.....).)))-).----- ( -31.60)
>DroPer_CAF1 18133 111 - 1
UAC----AACAUGUAUUUAUCCACUUGGUUAGUUAGAAACGGUUAAUGGC----AAAUGGUGCCAUUUAGCUUGUUCAACAAGAGUGGCUCUUUGUGGCUACAAAAUGCAGC-UAACCCC
...----...................((((((((.(((..((((((((((----(.....))))).))))))..))).......((((((......)))))).......)))-))))).. ( -29.90)
>consensus
UACCUUAAUGCGACUCUAAGCCAUAUAGUUAGCCAGGCAUUGCAACUGCCAUAAAAAACUUGGCAAUUAGCUUGUUUAACAAGAGCG_CUCUUUGUGGCUACAAAAUGCAGC_CACCU__
..................(((((((.((...((((((.....................)))))).....((((.........))))....)).))))))).................... (-16.40 = -16.85 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:07 2006