Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014772.1 Kokia drynarioides strain JFW-HI SEQ_129813, 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: 53370
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 172 characters in sequence are not A, C, G, or T
Found at i:11112 original size:72 final size:72
Alignment explanation
Indices: 11030--11174 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
11020 TCCTCTACAC
11030 TATCCTCTCCTCCTTATTGACAACTTGTATCAATAATCCTCTTGGAATATTAGTAATAGTTTTCT
1 TATCCTCTCCTCCTTATTGACAACTTGTATCAATAATCCTCTTGGAATATTAGTAATAGTTTTCT
11095 TTTAGAT
66 TTTAGAT
11102 TATCCTCTCCTCCTTATTGACAACTTGTATCAATAATCCTCTTGGAATATTAGTAATAGTTTTCT
1 TATCCTCTCCTCCTTATTGACAACTTGTATCAATAATCCTCTTGGAATATTAGTAATAGTTTTCT
11167 TTTAGAT
66 TTTAGAT
11174 T
1 T
11175 TAATGGTCAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (72 bp):
TATCCTCTCCTCCTTATTGACAACTTGTATCAATAATCCTCTTGGAATATTAGTAATAGTTTTCT
TTTAGAT
Found at i:12018 original size:21 final size:21
Alignment explanation
Indices: 11993--12048 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
11983 AAAAATGACA
* *
11993 AAAAAATATCGATACATTTTC
1 AAAAAGTATCGATACAGTTTC
12014 AAAAAGTATCGATACAGTTTC
1 AAAAAGTATCGATACAGTTTC
*
12035 AAAAAGTATTGATA
1 AAAAAGTATCGATA
12049 TCTTTTACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (21 bp):
AAAAAGTATCGATACAGTTTC
Found at i:13710 original size:13 final size:13
Alignment explanation
Indices: 13692--13720 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
13682 ATTAAGAAAA
13692 AGTGTCAAGTTTG
1 AGTGTCAAGTTTG
13705 AGTGTCAAGTTTG
1 AGTGTCAAGTTTG
13718 AGT
1 AGT
13721 ACCAAATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.07, G:0.31, T:0.38
Consensus pattern (13 bp):
AGTGTCAAGTTTG
Found at i:19799 original size:2 final size:2
Alignment explanation
Indices: 19792--19824 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19782 ATGAGTATAA
19792 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
19825 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:22034 original size:3 final size:3
Alignment explanation
Indices: 22026--22078 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
22016 AGCTCCTAAA
22026 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
22074 AAG AA
1 AAG AA
22079 AGAATCCATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:23881 original size:6 final size:6
Alignment explanation
Indices: 23872--23902 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
23862 ATAAAAAAGT
23872 GGAAGG GGAAGG GGAAGG GGAAGG GGAAGG G
1 GGAAGG GGAAGG GGAAGG GGAAGG GGAAGG G
23903 AAGAAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGAAGG
Found at i:25772 original size:2 final size:2
Alignment explanation
Indices: 25765--25790 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25755 TTAATAGATG
25765 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
25791 GCGAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30494 original size:68 final size:68
Alignment explanation
Indices: 30417--30552 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 68
30407 TTTATATCTA
*
30417 TATTTAAAAAAATAACCAAACTCCGTGTGTTGGCCTGATGGTCAAAAGTCTTAAGTGCGACTTGA
1 TATTTAAAAAAATAACCAAACTCCATGTGTTGGCCTGATGGTCAAAAGTCTTAAGTGCGACTTGA
30482 ATT
66 ATT
*
30485 TATTTAAAAAAATAATCAAACTCCATGTGTTGGCCTGATGGTCAAAAGTCTTAAGTGCGACTTGA
1 TATTTAAAAAAATAACCAAACTCCATGTGTTGGCCTGATGGTCAAAAGTCTTAAGTGCGACTTGA
30550 ATT
66 ATT
30553 CAAGTCGAAC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (68 bp):
TATTTAAAAAAATAACCAAACTCCATGTGTTGGCCTGATGGTCAAAAGTCTTAAGTGCGACTTGA
ATT
Found at i:39088 original size:17 final size:18
Alignment explanation
Indices: 39062--39103 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
39052 TGACAATGTC
39062 AAAA-AAAAAAAAAG-AA
1 AAAAGAAAAAAAAAGAAA
39078 AAAAGAAAAAAAAAGAAA
1 AAAAGAAAAAAAAAGAAA
39096 AAAAGAAA
1 AAAAGAAA
39104 TGTGCATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 4 0.17
17 10 0.42
18 10 0.42
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAAAAGAAA
Found at i:44432 original size:20 final size:20
Alignment explanation
Indices: 44396--44435 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
44386 TTATGATATA
*
44396 AAAATAAATATTTTATATCT
1 AAAATAAATATTATATATCT
44416 AAAATAATATATATATATAT
1 AAAATAA-ATAT-TATATAT
44436 ATATATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATAAATATTATATATCT
Found at i:48416 original size:21 final size:22
Alignment explanation
Indices: 48386--48431 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
48376 ATAACAAAAA
*
48386 TAATTGTAATTATAACTAG-AAT
1 TAATTGTAA-TATAAATAGAAAT
48408 TAATT-TAATATAAATAGAAAT
1 TAATTGTAATATAAATAGAAAT
48429 TAA
1 TAA
48432 ACAAAAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (22 bp):
TAATTGTAATATAAATAGAAAT
Done.