other hairpins
novel_cloningOK_nonpairedHIGH_bulgeHIGH (3 loci)
novel_cloningOK_shortStem (3 loci)
block4202 [novel_cloningOK_shortStem]
Hairpin parameters
| no | 0.357 | no | no | 0.62/0.68 | 19/21/0.80 | 0.0
| 0.0
| 4
| 0
| 1
| 0
| 2
| 14
| 5arm
| 3
| nd
| 0.29
| 2
| 5 | 1 | na | na |
| seed | ---GAUGGCG-------------------------------------------------------------------------- | 5 | novel |
| | | | CE1 |
| | --CGATGGCGGACAAGTCGGCTT------------------------------------------------------------- | 21 | 4 |
| | --CGATGGCGGACAAGTCGGC--------------------------------------------------------------- | 19 | 1 |
| celegans | aaCGATGGCGGACAAGTCGGCTTacatgggcgctggtggctatggatcgggctacatgggatccaatgcttcttcgtcaggtta | |
| | ************************************************************************************ | |
| | .........>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | C24D10.8 C24D10.8 nspd-6 |
| celegans | (((..(((((((.((((.((.((.(((((((.(((((........)))))))).)))).)).))...)))).))))))).))). | 0.850 -25.30 |
| celegans | chromosome:IV:5165637:5165720:-1 | Same_strand|Boundary_non-coding|C24D10.8|C24D10.8 ## C24D10.8|protein_coding|nspd-6|Nematode Specific Peptide family, group D family member (nspd-6) [Source:RefSeq_peptide;Acc:NP_001076664] ## {SimpF: WRM0633dC11 -1 fosmid,C24D10.8 -1 Expression_profile} |
block5518 [novel_cloningOK_shortStem]
Hairpin parameters
| no | 0.168 | no | no | 0.38/0.48 | 21/21/1.00 | 0.9
| 0.9
| 7
| 0
| 1
| 0
| 4
| 1
| 3arm
| 1
| nd
| 0.29
| 3
| 7 | 1 | na | na |
| seed | -------------------------------------------------------------GGAGUUG----------------- | 5 | novel |
| seed | ----------------------------------------------------------AUUGGAG-------------------- | 2 | novel |
| | | | CE1 |
| | ------------------------------------------------------------TGGAGTTGTTTCAGTCAGGTC---- | 21 | 5 |
| | ---------------------------------------------------------TATTGGAGTTGTTTCAGTCAG------- | 21 | 2 |
| celegans | gacacttttacccactgttttacgtattctattttcctcaactctattgaaatcaatTATTGGAGTTGTTTCAGTCAGGTCgtcc | |
| | ************************************************************************************* | |
| | ----------------------------------------------------------------------------------------------- | Y73B6BL.35 Y73B6BL.35 Y73B6BL.35 |
| celegans | (((......(((.((((.....................((((((((.(((......))).))))))))...))))..))).))). | 0.470 -12.65 |
| celegans | chromosome:IV:6413188:6413272:1 | Opposite_strand|Intronic_coding|Y73B6BL.35|Y73B6BL.35 ## Y73B6BL.35|protein_coding|Y73B6BL.35|Y73B6BL.35 [Source:RefSeq_peptide;Acc:NP_741424] ## {SimpF: WRM0631aB07 1 fosmid,WRM0614aD01 1 fosmid} |
block6169 [novel_cloningOK_shortStem]
Hairpin parameters
| no | 0.312 | no | no | 0.29/0.30 | 20/21/1.00 | 0.0
| 0.0
| 7
| 0
| 1
| 0
| 1
| 7
| 3arm
| 1
| nd
| 0.24
| 3
| 8 | 1 | na | na |
| seed | -------------------------------------------------UAUAUUU-------------- | 8 | novel |
| | | | CE1 |
| | ------------------------------------------------TTATATTTTCAGTCAAGTCGT- | 21 | 7 |
| | ------------------------------------------------TTATATTTTCAGTCAAGTCG-- | 20 | 1 |
| celegans | ccactgcttcattcaactgttatgtgttttaacgatttacagtttcaaTTATATTTTCAGTCAAGTCGTg | |
| | ********************************************************************** | |
| celegans | .(((.((((......((((..(((((....(((........))).....)))))...)))).)))).))) | 0.870 -9.00 |
novel_lenNOK_cloningOK (3 loci)
block3499 [novel_lenNOK_cloningOK]
Hairpin parameters
| no | 0.876 | no | no | 0.42/0.47 | 19/26/0.00 | 0.0
| 0.0
| 5
| 0
| 1
| 0
| 6
| 1
| 5arm
| 1
| nd
| 0.19
| 3
| 6 | 1 | na | na |
| seed | -------UUGAGAA------------------------------------------------------------ | 6 | novel |
| | | | CE1 |
| | ------GTTGAGAAAGTGGCTTGCTAAGTGTT------------------------------------------ | 26 | 5 |
| | ------GTTGAGAAAGTGGCTTGCT------------------------------------------------- | 19 | 1 |
| celegans | cgtattGTTGAGAAAGTGGCTTGCTAAGTGTTgaattcaatcaatagacgatgctgtctgtatctgaaaatcgc | |
| | ************************************************************************** | |
| celegans | ((.....((.(((.((((((((((((...((((....))))...))).))).)))).))...))).))...)). | 0.420 -10.90 |
| celegans | chromosome:III:3830844:3830917:1 | intergenic ## {SimpF: WRM065cE05 1 fosmid,C36A4.10 1 Expression_profile,WRM0624bD07 1 fosmid,WRM0640dH02 1 fosmid,WRM063dB07 1 fosmid,WRM0626aB12 1 fosmid,WRM062aH09 1 fosmid,WRM0634bH05 1 fosmid,WRM0613aC06 1 fosmid} |
block4267 [novel_lenNOK_cloningOK]
Hairpin parameters
| no | 0.084 | no | no | 0.33/0.33 | 18/18/0.00 | 0.0
| 0.0
| 6
| 0
| 1
| 0
| 12
| 9
| 3arm
| 1
| nd
| 0.00
| 0
| 6 | 1 | na | na |
| seed | -----------------------------------------------------------AAUGUGA---------------------- | 6 | novel |
| | | | CE1 |
| | ----------------------------------------------------------TAATGTGATTTTGGGTTG------------ | 18 | 6 |
| celegans | aaaaataattaactgtttcaaagttacattagatataatttgtgttcgagcattgcgaTAATGTGATTTTGGGTTGaaaaatgttttt | |
| | **************************************************************************************** | |
| celegans | (((((((.((((((....(((((((((((((..........((((....)))).....)))))))))))))))))))....))))))) | 0.860 -15.96 |
block6385 [novel_lenNOK_cloningOK]
Hairpin parameters
| no | 0.639 | no | no | 0.39/0.39 | 18/23/0.20 | 0.0 0.0
| 0.0 0.0
| 1 4
| 0 0
| 1 1
| 0 0
| 21 17
| -5 4
| 3arm_loop 3arm
| 1 1
| nd nd
| 0.35 0.22
| 4 1
| 5 | 1 | na | na |
| seed | ----------------------------------------------------------AAUUGGC--------------------------- | 4 | novel |
| seed | -------------------------------------------------AUCGGUU------------------------------------ | 1 | novel |
| | | | CE1 |
| | ---------------------------------------------------------GAATTGGCATGTTTCTCT----------------- | 18 | 4 |
| | ------------------------------------------------GATCGGTTTGAATTGGCATGTTT--------------------- | 23 | 1 |
| celegans | ggtactcgtcgaagttttccgaggaaacgaagttccactttccaacaagatcggtttGAATTGGCATGTTTCTCTgaaaaaaagattatatt | |
| | ******************************************************************************************** | |
| | <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<------------------------ | Y40B10A.1a Y40B10A.1 lbp-9 |
| | <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<........................ | Y40B10A.1b Y40B10A.1 lbp-9 |
| celegans | .......(((....(((((.((((((.....((.(((..(((.(((.......))).))).))).)).)))))).)))))...)))...... | 0.910 -15.90 |
| celegans | chromosome:V:2068545:2068636:-1 | Opposite_strand|Boundary_coding|Y40B10A.1a|Y40B10A.1 ## Opposite_strand|Boundary_non-coding|Y40B10A.1b|Y40B10A.1 ## Y40B10A.1|protein_coding|lbp-9|Fatty acid-binding protein homolog 9. [Source:UniProtKB/Swiss-Prot;Acc:Q965W1] ## {SimpF: Y40B10A.H -1 Expression_profile} |
novel_loopOverlap_randfoldOK_nonpairedHIGH_bulgeHIGH (3 loci)
block1376 [novel_loopOverlap_randfoldOK_nonpairedHIGH_bulgeHIGH]
Hairpin parameters
| no | 0.003 | no | no | 0.45/0.45 | 22/22/1.00 | 0.0
| 0.0
| 1
| 0
| 1
| 0
| 20
| -3
| 5arm_loop
| 1
| nd
| 0.32
| 4
| 1 | 1 | na | na |
| seed | ---------------------CACAAGU------------------------------------------------------------ | 1 | novel |
| | | | CE1 |
| | --------------------TCACAAGTCAAGACAGAGCTTC---------------------------------------------- | 22 | 1 |
| celegans | cttgtcctagtccagaagcaTCACAAGTCAAGACAGAGCTTCaccgttctgtcttgtaatgtgacgcgctactcttatatcggaggag | |
| | **************************************************************************************** | |
| celegans | (((.(((......(((.((.(((((...(((((((((((......)))))))))))...))))).)).....)))......))).))) | 0.930 -31.50 |
| celegans | chromosome:I:15064529:15064616:1 | intergenic ## {SimpF: WRM066aE11 1 fosmid,WRM068cA11 1 fosmid,WRM067aB07 1 fosmid,WRM0628aC12 1 fosmid,WRM0625cG10 1 fosmid,WRM0619bG03 1 fosmid,WRM0629dE08 1 fosmid,WRM0637dE09 1 fosmid,WRM0623dH11 1 fosmid,WRM0631aD12 1 fosmid,WRM0640bG08 1 fosmid,WRM0626cH01 1 fosmid,WRM0615cH09 1 fosmid} |
block5259 [novel_loopOverlap_randfoldOK_nonpairedHIGH_bulgeHIGH]
Hairpin parameters
| no | 0.004 | no | no | 0.41/0.41 | 22/22/1.00 | 0.0
| 0.0
| 1
| 0
| 1
| 0
| 31
| -2
| 5arm_loop
| 1
| nd
| 0.36
| 4
| 1 | 1 | na | na |
| seed | --------------------------------CUAGCCG---------------------------------------------------------------------- | 1 | novel |
| | | | CE1 |
| | -------------------------------GCTAGCCGAGAAGAAAATAACA-------------------------------------------------------- | 22 | 1 |
| celegans | agaaatcagattttatcctcgccgtctttccGCTAGCCGAGAAGAAAATAACAataaatttattttctcacaggttgtcggttttttttttttgaaaaatttgaattct | |
| | ************************************************************************************************************* | |
| celegans | ((((.(((((((((.((............(((.(((((....(((((((((........)))))))))....))))).)))............))))))))))).)))) | 0.980 -25.35 |
block7331 [novel_loopOverlap_randfoldOK_nonpairedHIGH_bulgeHIGH]
Hairpin parameters
| no | 0.001 | no | no | 0.35/0.35 | 23/23/1.00 | 0.0
| 0.0
| 1
| 0
| 1
| 0
| 31
| -3
| 3arm_loop
| 1
| nd
| 0.43
| 4
| 1 | 1 | na | na |
| seed | ---------------------------------------------------------UCGAAUA---------------------------------------------- | 1 | novel |
| | | | CE1 |
| | --------------------------------------------------------TTCGAATATTTTTTGGGTGTGGT------------------------------- | 23 | 1 |
| celegans | tcttcgttgattatcacaccttaaaaacatttagcttaacgagcgcccgaagttcgTTCGAATATTTTTTGGGTGTGGTcattgtaggcaaggtgtggtgataacgatga | |
| | ************************************************************************************************************** | |
| celegans | ((.(((((.(((((((((((((...........((((.(((((((((((((((((....))))....))))))))).....)))))))))))))))))))))))))).)) | 0.690 -38.50 |
| celegans | chromosome:V:12548212:12548321:1 | intergenic ## {SimpF: WRM0631aC03 1 fosmid,WRM0630cG01 1 fosmid,WRM0628cD03 1 fosmid,WRM067dA01 1 fosmid,WRM0636dC04 1 fosmid,WRM0610dC02 1 fosmid,WRM0629cA07 1 fosmid,WRM062bC01 1 fosmid,WRM0614dA08 1 fosmid,WRM0630cB10 1 fosmid,WRM0619cH03 1 fosmid,WRM0626aD09 1 fosmid,WRM0612bB10 1 fosmid,WRM0617cE03 1 fosmid,WRM0640cD02 1 fosmid} |
novel_cloningOK_loopOverlap_nonpairedHIGH_bulgeHIGH (2 loci)
block6340 [novel_cloningOK_loopOverlap_nonpairedHIGH_bulgeHIGH]
Hairpin parameters
| no | 0.170 | no | no | 0.43/0.50 | 20/24/1.00 | 0.0
| 0.0
| 7
| 0
| 1
| 0
| 29
| -3
| 5arm_loop_3arm
| 1
| nd
| 0.43
| 4
| 11 | 1 | na | na |
| seed | ------------------------------UUUGAAG--------------------------------------------------------------- | 7 | novel |
| seed | ---------------------------------GAAGAAG------------------------------------------------------------ | 2 | novel |
| seed | --------------------------------UGAAGAA------------------------------------------------------------- | 1 | novel |
| seed | -----------------------------AUUUGAA---------------------------------------------------------------- | 1 | novel |
| | | | CE1 |
| | -----------------------------ATTTGAAGAAGGTGGTAGCCTTG------------------------------------------------ | 23 | 7 |
| | --------------------------------TGAAGAAGGTGGTAGCCTTG------------------------------------------------ | 20 | 2 |
| | ----------------------------GATTTGAAGAAGGTGGTAGCCTTG------------------------------------------------ | 24 | 1 |
| | -------------------------------TTGAAGAAGGTGGTAGCCTTGAGG--------------------------------------------- | 24 | 1 |
| celegans | ttctagcttagcaagtttggtcgaagaagATTTGAAGAAGGTGGTAGCCTTGaggacactttcacaaataggtttttcaatagttactttgggcctaggg | |
| | **************************************************************************************************** | |
| celegans | .(((((((((..((((...((.((((((.(((((..(((((((....((....)).))))))).)))))...)))))).))....))))))))).)))). | 0.990 -24.50 |