Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004078.1 Kokia drynarioides strain JFW-HI SEQ_117245, 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: 28902
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Found at i:146 original size:86 final size:86
Alignment explanation
Indices: 1--515 Score: 940
Period size: 86 Copynumber: 6.0 Consensus size: 86
*
1 ATAATGTGTTGATTTGACAATACATTATTTATTAATTTTATATATTTAAATAAAAATTATTATTA
1 ATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTA
*
66 TTCTATTACAATTTTTATCAA
66 TTATATTACAATTTTTATCAA
*
87 ATAATGTGTTGATTTGACAATACATTATTTATTAATTTTATATATTTAAATAAAAATTATTATTA
1 ATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTA
152 TTATATTACAATTTTTATCAA
66 TTATATTACAATTTTTATCAA
173 ATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTA
1 ATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTA
238 TTATATTACAATTTTTATCAA
66 TTATATTACAATTTTTATCAA
*
259 ATAATGTGTTGATTTGACAATATATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTA
1 ATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTA
324 TTATATTACAATTTTTATCAA
66 TTATATTACAATTTTTATCAA
* *
345 ATAATGTGTTGATTTGACAGTACATTATTTATTAATTTTAAATATTTAAATAAAATTTATTATTA
1 ATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTA
* *
410 TAATATTACAATTTTTTTCAA
66 TTATATTACAATTTTTATCAA
* *
431 ATAATATGTTGATTTGACAATACATTATTTATTAATTTTATATATTTAAATAAAAATTATTATTA
1 ATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTA
496 TTATATTACAATTTTTATCA
66 TTATATTACAATTTTTATCA
516 TATTTTAAAT
Statistics
Matches: 415, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 415 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (86 bp):
ATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTA
TTATATTACAATTTTTATCAA
Found at i:2998 original size:30 final size:30
Alignment explanation
Indices: 2936--3026 Score: 112
Period size: 30 Copynumber: 3.1 Consensus size: 30
2926 TCCGTTTACT
* * * *
2936 TTTTAAATTTAATTTGTAATTTCATTTTTA
1 TTTTAAATTTAATTTCTAATTTCCTATATA
*
2966 TTTTAAATTTAATTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCCTATATA
**
2996 TTTT-AATTTTTTTTCTAATTTCCTATATA
1 TTTTAAATTTAATTTCTAATTTCCTATATA
3025 TT
1 TT
3027 GTAATTATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 24 0.44
30 30 0.56
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTCCTATATA
Found at i:4010 original size:60 final size:59
Alignment explanation
Indices: 3897--4316 Score: 345
Period size: 61 Copynumber: 7.1 Consensus size: 59
3887 AAAAGGGACC
*
3897 AAAAAATTTGCAATTTTTTTATCCGAGAAAAGGGAGTGTCGGCCATTGC-ATGGCCAACATA
1 AAAAAATTTGCAA-TTTTTT-TCCGAGAAAAGGGAGTGTCGGCCA-TGCAATGGCCAACACA
3958 AAAAAATTTGCAATTTTCTTATCCGAGAAAAGGGAGTGTC-GCCATTGC-ATGGCCAACACCA
1 AAAAAATTTGCAATTTT-TT-TCCGAGAAAAGGGAGTGTCGGCCA-TGCAATGGCCAACA-CA
* * * *
4019 AAAAATTTTGAAATTTTTTTCTCGAGAAAA-GGAGGTGTCGACCATGCAATGGCCAACACC
1 AAAAAATTTGCAATTTTTTTC-CGAGAAAAGGGA-GTGTCGGCCATGCAATGGCCAACACA
* *
4079 CAAAAA--TGCAATTTTTTT-CGAGAAAAGGGGGTGTCGGCCATGCAATGGCCAACACA
1 AAAAAATTTGCAATTTTTTTCCGAGAAAAGGGAGTGTCGGCCATGCAATGGCCAACACA
* ** * ** * *
4135 CAAAAA--TGCAATTTTTTTTTGAGAAAAGGG-GATGTCGACCATTTAATGACTAACACCA
1 AAAAAATTTGCAATTTTTTTCCGAGAAAAGGGAG-TGTCGGCCATGCAATGGCCAACA-CA
* ** * *
4193 AAAAATTTTG-AATTTTTTTTTCTC-A-AAAAGAGG-GTGTCGGCCATGCAATAACTAACACC
1 AAAAAATTTGCAA--TTTTTTTC-CGAGAAAAG-GGAGTGTCGGCCATGCAATGGCCAACACA
* ***
4252 AAAAAA--TGCAATTTTTTTTTCGAGAAAAAGGG-GTGTCGGCCATTTGATGGCCAA-ACA
1 AAAAAATTTGCAA-TTTTTTTCCGAG-AAAAGGGAGTGTCGGCCATGCAATGGCCAACACA
4309 AAAAAATT
1 AAAAAATT
4317 ATATTTTTTA
Statistics
Matches: 302, Mismatches: 35, Indels: 46
0.79 0.09 0.12
Matches are distributed among these distances:
56 52 0.17
57 49 0.16
58 37 0.12
59 18 0.06
60 71 0.24
61 75 0.25
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (59 bp):
AAAAAATTTGCAATTTTTTTCCGAGAAAAGGGAGTGTCGGCCATGCAATGGCCAACACA
Found at i:4112 original size:56 final size:58
Alignment explanation
Indices: 3894--4316 Score: 382
Period size: 60 Copynumber: 7.2 Consensus size: 58
3884 ATAAAAAGGG
*
3894 ACCAAAAAATTTGCAATTTTTTTATCCGAGAAAAGGGAGTGTCGGCCATTGC-ATGGCCAAC
1 ACCAAAAAA-TTGCAATTTTTTT-T-CGAGAAAAGGGGGTGTCGGCCA-TGCAATGGCCAAC
** * *
3955 ATAAAAAAATTTGCAATTTTCTTATCCGAGAAAAGGGAGTGTC-GCCATTGC-ATGGCCAAC
1 ACCAAAAAA-TTGCAATTTT-TT-TTCGAGAAAAGGGGGTGTCGGCCA-TGCAATGGCCAAC
* * *
4015 ACCAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGAGGTGTCGACCATGCAATGGCCAAC
1 ACCAAAAAA--TTGCAATTTTTTT-TCGAGAAAAGGGGGTGTCGGCCATGCAATGGCCAAC
*
4076 ACCCAAAAA-TGCAA-TTTTTTTCGAGAAAAGGGGGTGTCGGCCATGCAATGGCCAAC
1 ACCAAAAAATTGCAATTTTTTTTCGAGAAAAGGGGGTGTCGGCCATGCAATGGCCAAC
* * * ** * *
4132 A-CACAAAAA-TGCAATTTTTTTTTGAGAAAAGGGGATGTCGACCATTTAATGACTAAC
1 ACCA-AAAAATTGCAATTTTTTTTCGAGAAAAGGGGGTGTCGGCCATGCAATGGCCAAC
* * ** *
4189 ACCAAAAAATTTTG-AATTTTTTTTTCTCA-AAAAGAGGGTGTCGGCCATGCAATAACTAAC
1 ACCAAAAAA--TTGCAA-TTTTTTTTC-GAGAAAAGGGGGTGTCGGCCATGCAATGGCCAAC
* ***
4249 ACCAAAAAA-TGCAATTTTTTTTTCGAGAAAAAGGGGTGTCGGCCATTTGATGGCCAA-
1 ACCAAAAAATTGCAA-TTTTTTTTCGAGAAAAGGGGGTGTCGGCCATGCAATGGCCAAC
*
4306 ACAAAAAAATT
1 ACCAAAAAATT
4317 ATATTTTTTA
Statistics
Matches: 305, Mismatches: 40, Indels: 37
0.80 0.10 0.10
Matches are distributed among these distances:
55 1 0.00
56 45 0.15
57 58 0.19
58 41 0.13
59 3 0.01
60 88 0.29
61 66 0.22
62 2 0.01
63 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (58 bp):
ACCAAAAAATTGCAATTTTTTTTCGAGAAAAGGGGGTGTCGGCCATGCAATGGCCAAC
Found at i:13039 original size:87 final size:87
Alignment explanation
Indices: 12945--13110 Score: 219
Period size: 87 Copynumber: 1.9 Consensus size: 87
12935 AGTAATTGAG
* * * * *
12945 TTTTTTTTCACTT-ATTTAGGTATTTAAACTTATAAAATATATTAAAAAGACTTTTAAACCTTTT
1 TTTTTTTTCA-TTCAATTAGGTATTTAAACTTATAAAATACAGTAAAAA-ACCTTCAAACCTTTT
13009 AAAAAAAA-TAATTAAGCTGTTAT
64 AAAAAAAAGTAATTAAGCTGTTAT
* * **
13032 TTTTTTTTCATTCAATTGGGTATTTAAACTTTTAAAATACAGTAAAAAACCTTCAAATTTTTTAA
1 TTTTTTTTCATTCAATTAGGTATTTAAACTTATAAAATACAGTAAAAAACCTTCAAACCTTTTAA
13097 AAAAAAGTAATTAA
66 AAAAAAGTAATTAA
13111 ACTCTTGCTT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
86 21 0.31
87 47 0.69
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.43
Consensus pattern (87 bp):
TTTTTTTTCATTCAATTAGGTATTTAAACTTATAAAATACAGTAAAAAACCTTCAAACCTTTTAA
AAAAAAGTAATTAAGCTGTTAT
Found at i:13217 original size:47 final size:46
Alignment explanation
Indices: 13135--13230 Score: 113
Period size: 47 Copynumber: 2.1 Consensus size: 46
13125 TAAAAATATA
* * * * *
13135 AAAAAATTTAAAATCAATAAAGATTATAAATATTATTAAATTTTAAT
1 AAAAAATTAAAAATCAATAAAAAATATAAAAATTATAAAATTTT-AT
*
13182 AAAAAATTAAAAATC-GTAAAAAATATAAAAAATTATAAAATTTTAT
1 AAAAAATTAAAAATCAATAAAAAATAT-AAAAATTATAAAATTTTAT
13228 AAA
1 AAA
13231 GTGATAAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
46 13 0.31
47 29 0.69
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (46 bp):
AAAAAATTAAAAATCAATAAAAAATATAAAAATTATAAAATTTTAT
Found at i:13292 original size:48 final size:46
Alignment explanation
Indices: 13166--13292 Score: 105
Period size: 48 Copynumber: 2.7 Consensus size: 46
13156 GATTATAAAT
* * *
13166 ATTATTAAATTTTAATAAAAAAT-TAAAAATCGTAAAAAATATAAAAA
1 ATTA-TAAAATTTAA-AAAAATTATAAAAATTGTAAAAAATATAAAAA
* * * * *
13213 ATTATAAAATTTTATAAAGTGATAAAGAAATTGTACAAAATATAAAGAA
1 ATTATAAAATTTAAAAAAATTAT-AA-AAATTGTAAAAAATATAAA-AA
13262 A-TATAAAATTCGTAAAAAAATTATAAAAATT
1 ATTATAAAATT--TAAAAAAATTATAAAAATT
13293 ATCGAACCAA
Statistics
Matches: 62, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
45 3 0.05
46 9 0.15
47 6 0.10
48 31 0.50
49 5 0.08
50 8 0.13
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (46 bp):
ATTATAAAATTTAAAAAAATTATAAAAATTGTAAAAAATATAAAAA
Found at i:13360 original size:17 final size:17
Alignment explanation
Indices: 13327--13360 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
13317 AATTTTTCTA
*
13327 TAATTTTTATTGATTTT
1 TAATTTTTATTCATTTT
13344 TAATTTTTA-TCATTTT
1 TAATTTTTATTCATTTT
13360 T
1 T
13361 CATCACATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TAATTTTTATTCATTTT
Done.