Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009914.1 Kokia drynarioides strain JFW-HI SEQ_124654, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19538
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:240 original size:25 final size:23
Alignment explanation
Indices: 212--257 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
202 GTTGGATCCA
212 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
237 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
258 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:344 original size:13 final size:13
Alignment explanation
Indices: 323--356 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
313 ATAATATAAT
323 AATAATAATCCTA
1 AATAATAATCCTA
*
336 AATATTAATCCTA
1 AATAATAATCCTA
*
349 AAAAATAA
1 AATAATAA
357 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:4282 original size:93 final size:93
Alignment explanation
Indices: 4123--4306 Score: 350
Period size: 93 Copynumber: 2.0 Consensus size: 93
4113 AAACCTGATA
* *
4123 TTCAACAATAACCCTGAAACCTTACAGTCTAAATCCTTTAAATTTGTCCCTCAAAAACCCAGATT
1 TTCAACAATAACCCTAAAACCTTAAAGTCTAAATCCTTTAAATTTGTCCCTCAAAAACCCAGATT
4188 CATCTTCCTGCATCATAAAGATAAAATG
66 CATCTTCCTGCATCATAAAGATAAAATG
4216 TTCAACAATAACCCTAAAACCTTAAAGTCTAAATCCTTTAAATTTGTCCCTCAAAAACCCAGATT
1 TTCAACAATAACCCTAAAACCTTAAAGTCTAAATCCTTTAAATTTGTCCCTCAAAAACCCAGATT
4281 CATCTTCCTGCATCATAAAGATAAAA
66 CATCTTCCTGCATCATAAAGATAAAA
4307 GAATTCAAGA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.29
Consensus pattern (93 bp):
TTCAACAATAACCCTAAAACCTTAAAGTCTAAATCCTTTAAATTTGTCCCTCAAAAACCCAGATT
CATCTTCCTGCATCATAAAGATAAAATG
Found at i:7588 original size:3 final size:3
Alignment explanation
Indices: 7582--7617 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
7572 CATTGATTCT
7582 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
7618 GCTTTTGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:11015 original size:5 final size:5
Alignment explanation
Indices: 11005--11038 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
10995 TTAACACATC
11005 TGCTA TGCTA TGCTA TGCTA TGCTA TGCTA TGCT
1 TGCTA TGCTA TGCTA TGCTA TGCTA TGCTA TGCT
11039 TGAGTGTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (5 bp):
TGCTA
Found at i:14103 original size:17 final size:17
Alignment explanation
Indices: 14081--14114 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
14071 TTAATTATCG
14081 TTATAATAAAAAATTAA
1 TTATAATAAAAAATTAA
**
14098 TTATAATTGAAAATTAA
1 TTATAATAAAAAATTAA
14115 ATCTAAAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TTATAATAAAAAATTAA
Done.