Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000446.1 Kokia drynarioides strain JFW-HI SEQ_111295, 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: 68996
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:503 original size:19 final size:20
Alignment explanation
Indices: 470--523 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
460 ATTAAGTATA
*
470 TTATT-ATATTTAAATTT-T
1 TTATTAATATTAAAATTTAT
488 TTATTAATATTAAAATTTAT
1 TTATTAATATTAAAATTTAT
* *
508 TTAGTAA-AATAAAATT
1 TTATTAATATTAAAATT
524 ATAACATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.16
19 19 0.61
20 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTATTAATATTAAAATTTAT
Found at i:18863 original size:4 final size:4
Alignment explanation
Indices: 18854--18879 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
18844 TTAGAATTGG
18854 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
18880 ATTTTGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:20006 original size:6 final size:6
Alignment explanation
Indices: 19995--20029 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
19985 ACTCAATTTA
19995 CTATTC CTATTC CTATTC CTATTC CTATTC CTATT
1 CTATTC CTATTC CTATTC CTATTC CTATTC CTATT
20030 TATATATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.51
Consensus pattern (6 bp):
CTATTC
Found at i:21372 original size:16 final size:17
Alignment explanation
Indices: 21351--21384 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21341 ACTCTTTATT
*
21351 AATTTT-AATATTTTTA
1 AATTTTAAATAATTTTA
21367 AATTTTAAATAATTTTA
1 AATTTTAAATAATTTTA
21384 A
1 A
21385 TAAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTTAAATAATTTTA
Found at i:25381 original size:6 final size:6
Alignment explanation
Indices: 25370--25394 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
25360 AACTAGCTAT
25370 TAGCCA TAGCCA TAGCCA TAGCCA T
1 TAGCCA TAGCCA TAGCCA TAGCCA T
25395 GCTTTTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (6 bp):
TAGCCA
Found at i:26715 original size:20 final size:20
Alignment explanation
Indices: 26664--26715 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
26654 TGATTATAAT
* * *
26664 TTAATTAATAATGTTTTTTCC
1 TTAATTAATCAT-ATTTTTAC
*
26685 TTGATTAATCATATTTTTAC
1 TTAATTAATCATATTTTTAC
*
26705 TTAATTCATCA
1 TTAATTAATCA
26716 AAGTATAACA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.54
Consensus pattern (20 bp):
TTAATTAATCATATTTTTAC
Found at i:32070 original size:2 final size:2
Alignment explanation
Indices: 32063--32093 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
32053 AAGGGAAGTA
*
32063 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32094 GGTATGTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47922 original size:21 final size:21
Alignment explanation
Indices: 47898--47943 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
47888 TATCATATTG
*
47898 TATTTTATGATATGCTAATTA
1 TATTTAATGATATGCTAATTA
47919 TATTTAATGATATGCTAATTA
1 TATTTAATGATATGCTAATTA
47940 TATT
1 TATT
47944 AATTTACTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (21 bp):
TATTTAATGATATGCTAATTA
Found at i:49555 original size:13 final size:13
Alignment explanation
Indices: 49537--49561 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49527 GAAATTCACT
49537 TATTATTTTGCAG
1 TATTATTTTGCAG
49550 TATTATTTTGCA
1 TATTATTTTGCA
49562 ATGTATAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.56
Consensus pattern (13 bp):
TATTATTTTGCAG
Found at i:50844 original size:15 final size:16
Alignment explanation
Indices: 50824--50853 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
50814 TTTGCATGCC
50824 ATTCCTT-TATTTATT
1 ATTCCTTGTATTTATT
50839 ATTCCTTGTATTTAT
1 ATTCCTTGTATTTAT
50854 CTTCCACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.20, C:0.13, G:0.03, T:0.63
Consensus pattern (16 bp):
ATTCCTTGTATTTATT
Found at i:55096 original size:23 final size:24
Alignment explanation
Indices: 55063--55117 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
55053 TTTTAATAAA
55063 TTTTTAGATTTTAAAAAT-ATTATT
1 TTTTTA-ATTTTAAAAATAATTATT
**
55087 TTTTTAATTTTTTAAATAATTATT
1 TTTTTAATTTTAAAAATAATTATT
55111 TTTTTAA
1 TTTTTAA
55118 CTTTGTTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTTTAATTTTAAAAATAATTATT
Found at i:55131 original size:24 final size:23
Alignment explanation
Indices: 55081--55134 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
55071 TTTTAAAAAT
*
55081 ATTATTTTTTTAATTTTTTAAATA
1 ATTATTTTTTTAATTTTTT-AACA
55105 ATTATTTTTTTAACTTTGTTT-ACA
1 ATTATTTTTTTAA-TTT-TTTAACA
55129 ATTATT
1 ATTATT
55135 GTCAATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 21 0.78
25 3 0.11
26 3 0.11
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (23 bp):
ATTATTTTTTTAATTTTTTAACA
Found at i:61405 original size:9 final size:9
Alignment explanation
Indices: 61391--61416 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
61381 TGATGAATCA
61391 AGGTTCAAG
1 AGGTTCAAG
61400 AGGTTCAAG
1 AGGTTCAAG
61409 AGGTTCAA
1 AGGTTCAA
61417 CAGTAACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.31, T:0.23
Consensus pattern (9 bp):
AGGTTCAAG
Found at i:67135 original size:24 final size:24
Alignment explanation
Indices: 67055--67123 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
67045 AATCTTTTAG
*
67055 TTAAACTCTGTTTAATTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
*
67079 TTAAACTCTATTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
67103 TTAAACTCTGTTTATTTGTTT
1 TTAAACTCTGTTTATTTGTTT
67124 GAGTCAAACT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.55
Consensus pattern (24 bp):
TTAAACTCTGTTTATTTGTTTCAA
Found at i:67443 original size:16 final size:16
Alignment explanation
Indices: 67418--67449 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
67408 TTGTGTGTTC
*
67418 AATTTTTCAATTTCTT
1 AATTTCTCAATTTCTT
67434 AATTTCTCAATTTCTT
1 AATTTCTCAATTTCTT
67450 TCGCTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTTCTCAATTTCTT
Done.