----------------------------
RANK 1

17 bp region
-12.933 kcal/mol at 37C (approx for the isolated helix)

top 5'-3' (scaffold base index 222-238; 5' scaffold base has index 0)
GCCTGGTTTCCGGCACC
(((.(.(((((((((((
CGGTCGAAAGGCCGTGG
bottom 3'-5' (scaffold base index 261-245; 5' scaffold base has index 0)

FASTA format:
>rank1_intra_scaffold
GCCTGGTTTCCGGCACC+GGTGCCGGAAAGCTGGC
(((.(.(((((((((((+))))))))))).).)))

----------------------------
RANK 2

11 bp region
-8.932 kcal/mol at 37C (approx for the isolated helix)

top 5'-3' (scaffold base index 509-519; 5' scaffold base has index 0)
CAAAAATTTAA
((((.((((((
GTTTATAAATT
bottom 3'-5' (scaffold base index 563-553; 5' scaffold base has index 0)

FASTA format:
>rank2_intra_scaffold
CAAAAATTTAA+TTAAATATTTG
((((.((((((+)))))).))))

----------------------------
RANK 3

8 bp region
-8.861 kcal/mol at 37C (approx for the isolated helix)

top 5'-3' (scaffold base index 443-450; 5' scaffold base has index 0)
ACAGGAAG
((((((((
TGTCCTTC
bottom 3'-5' (scaffold base index 581-574; 5' scaffold base has index 0)

FASTA format:
>rank3_intra_scaffold
ACAGGAAG+CTTCCTGT
((((((((+))))))))

----------------------------
RANK 4

18 bp region
-8.194 kcal/mol at 37C (approx for the isolated helix)

top 5'-3' (scaffold base index 299-316; 5' scaffold base has index 0)
CCCCTCAAACTGGCAGAT
((((..((((.((.((((
GGGGTTTTTGTCCTTCTA
bottom 3'-5' (scaffold base index 589-572; 5' scaffold base has index 0)

FASTA format:
>rank4_intra_scaffold
CCCCTCAAACTGGCAGAT+ATCTTCCTGTTTTTGGGG
((((..((((.((.((((+)))).)).))))..))))

----------------------------
RANK 5

12 bp region
-8.052 kcal/mol at 37C (approx for the isolated helix)

top 5'-3' (scaffold base index 273-284; 5' scaffold base has index 0)
CTTCCTGAGGCC
(((((((..(((
GAAGGACATCGG
bottom 3'-5' (scaffold base index 450-439; 5' scaffold base has index 0)

FASTA format:
>rank5_intra_scaffold
CTTCCTGAGGCC+GGCTACAGGAAG
(((((((..(((+)))..)))))))

----------------------------
RANK 6

12 bp region
-8.052 kcal/mol at 37C (approx for the isolated helix)

top 5'-3' (scaffold base index 529-540; 5' scaffold base has index 0)
TAACAAAATATT
(((..(((((((
ATTCGTTTATAA
bottom 3'-5' (scaffold base index 567-556; 5' scaffold base has index 0)

FASTA format:
>rank6_intra_scaffold
TAACAAAATATT+AATATTTGCTTA
(((..(((((((+)))))))..)))

----------------------------
RANK 7

13 bp region
-7.693 kcal/mol at 37C (approx for the isolated helix)

top 5'-3' (scaffold base index 135-147; 5' scaffold base has index 0)
CCTTTCGCCAGCT
(((.(.(((((((
GGACATCGGTCGA
bottom 3'-5' (scaffold base index 447-435; 5' scaffold base has index 0)

FASTA format:
>rank7_intra_scaffold
CCTTTCGCCAGCT+AGCTGGCTACAGG
(((.(.(((((((+))))))).).)))

----------------------------
RANK 8

10 bp region
-7.622 kcal/mol at 37C (approx for the isolated helix)

top 5'-3' (scaffold base index 445-454; 5' scaffold base has index 0)
AGGAAGGCCA
(((((.((((
TCCTTGCGGT
bottom 3'-5' (scaffold base index 482-473; 5' scaffold base has index 0)

FASTA format:
>rank8_intra_scaffold
AGGAAGGCCA+TGGCGTTCCT
(((((.((((+)))).)))))

----------------------------
RANK 9

10 bp region
-7.622 kcal/mol at 37C (approx for the isolated helix)

top 5'-3' (scaffold base index 484-493; 5' scaffold base has index 0)
TTGGTTAAAA
((.(((((((
AAACAATTTT
bottom 3'-5' (scaffold base index 535-526; 5' scaffold base has index 0)

FASTA format:
>rank9_intra_scaffold
TTGGTTAAAA+TTTTAACAAA
((.(((((((+))))))).))

----------------------------
RANK 10

10 bp region
-7.622 kcal/mol at 37C (approx for the isolated helix)

top 5'-3' (scaffold base index 135-144; 5' scaffold base has index 0)
CCTTTCGCCA
((.(((((((
GGTAAGCGGT
bottom 3'-5' (scaffold base index 215-206; 5' scaffold base has index 0)

FASTA format:
>rank10_intra_scaffold
CCTTTCGCCA+TGGCGAATGG
((.(((((((+))))))).))

