Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006804.1 Kokia drynarioides strain JFW-HI SEQ_121403, 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: 24484
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:232 original size:32 final size:33
Alignment explanation
Indices: 193--282 Score: 109
Period size: 32 Copynumber: 2.9 Consensus size: 33
183 AATGCCTTTT
* *
193 TTATTATTAATTATTATTATTTTT-AAAAGATA
1 TTATTATTAATTATTATTATTTTTAAAAAAAAA
*
225 TTATTATT-ATTATTATTGTTTTTAAAAAAAAA
1 TTATTATTAATTATTATTATTTTTAAAAAAAAA
*
257 TTATTATTAA-TA--AATATTTTTAAAAA
1 TTATTATTAATTATTATTATTTTTAAAAA
283 TTGCCCACTC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
30 12 0.24
31 14 0.27
32 24 0.47
33 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (33 bp):
TTATTATTAATTATTATTATTTTTAAAAAAAAA
Found at i:964 original size:22 final size:23
Alignment explanation
Indices: 922--978 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
912 TAGACTTTTC
* *
922 TAAATTTAATTTTATAATAAATT
1 TAAATTTAAATTTATAATAAACT
945 TAAATTTAAATTT-TAATAAACT
1 TAAATTTAAATTTATAATAAACT
967 TAAATTTTAAAT
1 TAAA-TTTAAAT
979 AAACTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 12 0.39
23 19 0.61
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAATTTAAATTTATAATAAACT
Found at i:981 original size:17 final size:17
Alignment explanation
Indices: 945--998 Score: 83
Period size: 17 Copynumber: 3.2 Consensus size: 17
935 ATAATAAATT
*
945 TAAATTTAAATTTT-AA
1 TAAACTTAAATTTTAAA
961 TAAACTTAAATTTTAAA
1 TAAACTTAAATTTTAAA
*
978 TAAACTTAAATTTAAAA
1 TAAACTTAAATTTTAAA
995 TAAA
1 TAAA
999 TTCAATTCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
16 13 0.37
17 22 0.63
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAACTTAAATTTTAAA
Found at i:3400 original size:18 final size:18
Alignment explanation
Indices: 3377--3422 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
3367 CTATTGTGGC
3377 TGCATCTGGTTATATGAT
1 TGCATCTGGTTATATGAT
* * *
3395 TGCATCTGATTTTGTGAT
1 TGCATCTGGTTATATGAT
*
3413 TGCAACTGGT
1 TGCATCTGGT
3423 CAGCTTGTGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.20, C:0.13, G:0.24, T:0.43
Consensus pattern (18 bp):
TGCATCTGGTTATATGAT
Found at i:23335 original size:12 final size:12
Alignment explanation
Indices: 23318--23360 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
23308 ATTAAGGCAG
23318 AAGAAGAAAGAA
1 AAGAAGAAAGAA
23330 AAGAAG-AAGAA
1 AAGAAGAAAGAA
23341 AAGGAAGAAA-AA
1 AA-GAAGAAAGAA
23353 GAAGAAGA
1 -AAGAAGA
23361 CGTTACCTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 7 0.25
12 17 0.61
13 4 0.14
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAGAA
Found at i:23788 original size:17 final size:17
Alignment explanation
Indices: 23768--23823 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
23758 ATTGTCATTA
23768 CATTTTTATTGTCTCTG
1 CATTTTTATTGTCTCTG
23785 CA-TTTTACTTGT-TCTCG
1 CATTTTTA-TTGTCTCT-G
*
23802 CATTTTCATTGTCGT-TG
1 CATTTTTATTGTC-TCTG
23819 CATTT
1 CATTT
23824 CCATTAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
16 8 0.24
17 19 0.58
18 5 0.15
19 1 0.03
ACGTcount: A:0.12, C:0.20, G:0.12, T:0.55
Consensus pattern (17 bp):
CATTTTTATTGTCTCTG
Found at i:24429 original size:16 final size:15
Alignment explanation
Indices: 24390--24430 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
24380 AGTCACATAT
24390 ATAAAAAA-AAAGAG
1 ATAAAAAAGAAAGAG
24404 A-AAAAAAGAAAGAG
1 ATAAAAAAGAAAGAG
24418 ATAAAGAAAGAAA
1 ATAAA-AAAGAAA
24431 AGTTGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.25
14 8 0.33
15 3 0.12
16 7 0.29
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (15 bp):
ATAAAAAAGAAAGAG
Found at i:24457 original size:2 final size:2
Alignment explanation
Indices: 24450--24484 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
24440 AAAGAAATAC
24450 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.