Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011664.1 Kokia drynarioides strain JFW-HI SEQ_126656, 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: 19390
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Warning! 108 characters in sequence are not A, C, G, or T
Found at i:1700 original size:29 final size:29
Alignment explanation
Indices: 1646--1734 Score: 110
Period size: 29 Copynumber: 3.0 Consensus size: 29
1636 TTTTAAAATT
1646 ATTTTAAATTATTTTTTTAAAATATAAAAA
1 ATTTTAAATTA-TTTTTTAAAATATAAAAA
1676 ATTTTAAATTATTTTTTAAAATAT--AAA
1 ATTTTAAATTATTTTTTAAAATATAAAAA
*
1703 ATTATTAAAAATATTGTTTTAAAATAATAAAA
1 ATT-TT-AAATTATT-TTTTAAAAT-ATAAAA
1735 TTATTGAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
27 6 0.12
28 2 0.04
29 20 0.38
30 20 0.38
31 2 0.04
33 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
ATTTTAAATTATTTTTTAAAATATAAAAA
Found at i:1736 original size:31 final size:29
Alignment explanation
Indices: 1639--1749 Score: 118
Period size: 30 Copynumber: 3.7 Consensus size: 29
1629 TGAATGATTT
1639 TAAAATTATTTTAAATTATTTTTTTAAAATATA
1 TAAAATTA--TTAAATTA-TTTTTTAAAATA-A
*
1672 AAAAATT-TTAAATTATTTTTTAAAAT-A
1 TAAAATTATTAAATTATTTTTTAAAATAA
*
1699 TAAAATTATTAAAAATATTGTTTTAAAATAA
1 TAAAATTATT-AAATTATT-TTTTAAAATAA
* *
1730 TAAAATTATTGAATAATTTT
1 TAAAATTATTAAATTATTTT
1750 AATTTTCAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
27 7 0.10
28 2 0.03
29 20 0.29
30 22 0.32
31 11 0.16
33 6 0.09
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
TAAAATTATTAAATTATTTTTTAAAATAA
Found at i:2670 original size:27 final size:28
Alignment explanation
Indices: 2640--2713 Score: 116
Period size: 27 Copynumber: 2.6 Consensus size: 28
2630 GATGATTATT
2640 ATAATTTTAATAATTTTATATTTT-AAA
1 ATAATTTTAATAATTTTATATTTTAAAA
2667 ATAATTTTAA-AATTTTTATATTTTAAAAA
1 ATAATTTTAATAA-TTTTATATTTT-AAAA
2696 ATAATTTTAATAATTTTA
1 ATAATTTTAATAATTTTA
2714 AAATCATTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
26 2 0.05
27 21 0.49
29 18 0.42
30 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATAATTTTAATAATTTTATATTTTAAAA
Found at i:3794 original size:17 final size:17
Alignment explanation
Indices: 3772--3806 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3762 AAATTCTTTA
3772 AACAATAGTT-TTAAAAT
1 AACAATA-TTGTTAAAAT
3789 AACAATATTGTTAAAAT
1 AACAATATTGTTAAAAT
3806 A
1 A
3807 TATTTGATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (17 bp):
AACAATATTGTTAAAAT
Found at i:6790 original size:29 final size:29
Alignment explanation
Indices: 6758--7029 Score: 145
Period size: 29 Copynumber: 9.3 Consensus size: 29
6748 AAAGTCAAAC
6758 TTTTGGAAAGTTGAGGGT-AAAATGGTAAT
1 TTTTGGAAAGTTGAGGGTAAAAAT-GTAAT
* * *
6787 TTTTGG-ATGCTCGAGGGT-AAAATGGTGAT
1 TTTTGGAAAG-TTGAGGGTAAAAAT-GTAAT
* * * *
6816 TTTTTG-AAGTTCGGGGGGCAAAAATATAAT
1 TTTTGGAAAGTT--GAGGGTAAAAATGTAAT
*
6846 TTTT-GAGAAGTTCGAGGGTAAAAATGTGAT
1 TTTTGGA-AAGTT-GAGGGTAAAAATGTAAT
* * *
6876 TTTTAG-AAGTATGGGGGTAAAAAAAGT-AT
1 TTTTGGAAAGT-TGAGGGT-AAAAATGTAAT
* *
6905 TTTT-GAAAGTTCAGGGGTAAAAATATAA-
1 TTTTGGAAAGTTGA-GGGTAAAAATGTAAT
* * * *
6933 TTTTGGAAAGTTCGAGGATCAAAATTTATT
1 TTTTGGAAAGTT-GAGGGTAAAAATGTAAT
* *
6963 TTTTAG-AAGTTTAGGAGT-AAAATGTAAT
1 TTTTGGAAAGTTGAGG-GTAAAAATGTAAT
*
6991 TTTT-GAGAAGTTTGAGGAGTAAAAATGTGAT
1 TTTTGGA-AAG-TTGAGG-GTAAAAATGTAAT
7022 TTTTGGAA
1 TTTTGGAA
7030 GTTCGTGCAC
Statistics
Matches: 189, Mismatches: 33, Indels: 40
0.72 0.13 0.15
Matches are distributed among these distances:
27 1 0.01
28 30 0.16
29 81 0.43
30 50 0.26
31 25 0.13
32 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
TTTTGGAAAGTTGAGGGTAAAAATGTAAT
Found at i:6865 original size:60 final size:59
Alignment explanation
Indices: 6782--6926 Score: 158
Period size: 59 Copynumber: 2.5 Consensus size: 59
6772 GGGTAAAATG
* * * *
6782 GTAATTTTTG-GATGCTCGAGGGTAAAATGGTGATTTTTTGAAGT-TCGGGGGGCAAAAATA
1 GTAATTTTTGAGAAGTTCGAGGGTAAAAT-GTGATTTTTAGAAGTAT--GGGGGCAAAAAAA
*
6842 -TAATTTTTGAGAAGTTCGAGGGTAAAAATGTGATTTTTAGAAGTATGGGGGTAAAAAAA
1 GTAATTTTTGAGAAGTTCGAGGGT-AAAATGTGATTTTTAGAAGTATGGGGGCAAAAAAA
6901 GT-ATTTTTGA-AAGTTC-AGGGGTAAAA
1 GTAATTTTTGAGAAGTTCGA-GGGTAAAA
6927 ATATAATTTT
Statistics
Matches: 75, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
57 5 0.07
58 10 0.13
59 28 0.37
60 26 0.35
61 6 0.08
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (59 bp):
GTAATTTTTGAGAAGTTCGAGGGTAAAATGTGATTTTTAGAAGTATGGGGGCAAAAAAA
Found at i:6983 original size:87 final size:88
Alignment explanation
Indices: 6816--6984 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 88
6806 AAATGGTGAT
* * *
6816 TTTTTGAAGTTCGGGGGGCAAAAATATAATTTTTGAGAAGTTCGAGGGTAAAAATGTGATTTTTA
1 TTTTTGAAGTTCGAGGGGCAAAAATATAATTTTGGAGAAGTTCGAGGATAAAAATGTGATTTTTA
* *
6881 GAAGTATGGGGGTAAAAAAAGTA
66 GAAGTATAGGAGTAAAAAAAGTA
* * *
6904 TTTTTGAAAGTTC-AGGGGTAAAAATATAATTTTGGA-AAGTTCGAGGATCAAAAT-TTATTTTT
1 TTTTTG-AAGTTCGAGGGGCAAAAATATAATTTTGGAGAAGTTCGAGGATAAAAATGTGA-TTTT
*
6966 TAGAAGTTTAGGAGTAAAA
64 TAGAAGTATAGGAGTAAAA
6985 TGTAATTTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
86 2 0.03
87 36 0.51
88 26 0.37
89 6 0.09
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (88 bp):
TTTTTGAAGTTCGAGGGGCAAAAATATAATTTTGGAGAAGTTCGAGGATAAAAATGTGATTTTTA
GAAGTATAGGAGTAAAAAAAGTA
Found at i:8381 original size:30 final size:31
Alignment explanation
Indices: 8325--8485 Score: 159
Period size: 31 Copynumber: 5.3 Consensus size: 31
8315 AAAATTGTTT
* * *
8325 TTTGACTCTTAAATTTTCCAAAAAAATT-GAA
1 TTTGACCCCTAAATTTT-CTAAAAAATTCGAA
*
8356 TTTGACCCCTAAATTTTCTAAAAAATTTGAA
1 TTTGACCCCTAAATTTTCTAAAAAATTCGAA
* *
8387 TTTGACCCCTAAATTTTCCAAAAAATTCTAA
1 TTTGACCCCTAAATTTTCTAAAAAATTCGAA
* * * * *
8418 TTTGACCTCTAAACTTTCT-AGAACTTCCAA
1 TTTGACCCCTAAATTTTCTAAAAAATTCGAA
*
8448 TTTGACCCCTAAAATTTTC--AAAAATTCAAA
1 TTTGACCCCT-AAATTTTCTAAAAAATTCGAA
*
8478 ATTGACCC
1 TTTGACCC
8486 GATTTTAAAT
Statistics
Matches: 110, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
30 41 0.37
31 69 0.63
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (31 bp):
TTTGACCCCTAAATTTTCTAAAAAATTCGAA
Found at i:9425 original size:16 final size:16
Alignment explanation
Indices: 9378--9426 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
9368 AATTCATGGG
*
9378 TAAATT-TAAAATTAAT
1 TAAATTGTAAAAAT-AT
9394 TAAAATTGTAAAAAATAT
1 T-AAATTGT-AAAAATAT
9412 TAAATTGTAAAAATA
1 TAAATTGTAAAAATA
9427 AAAAAAGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 8 0.28
17 12 0.41
18 4 0.14
19 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (16 bp):
TAAATTGTAAAAATAT
Found at i:9807 original size:40 final size:41
Alignment explanation
Indices: 9757--9842 Score: 156
Period size: 40 Copynumber: 2.1 Consensus size: 41
9747 ATTTGGTTTT
*
9757 TAAATCCTTGTTTACAATGATTATGTTTTGTTTTTCTCAAA
1 TAAATCCTTGTTTACAATGATCATGTTTTGTTTTTCTCAAA
9798 TAAA-CCTTGTTTACAATGATCATGTTTTGTTTTTCTCAAA
1 TAAATCCTTGTTTACAATGATCATGTTTTGTTTTTCTCAAA
9838 TAAAT
1 TAAAT
9843 GCCTGTCTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
40 39 0.91
41 4 0.09
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (41 bp):
TAAATCCTTGTTTACAATGATCATGTTTTGTTTTTCTCAAA
Found at i:10019 original size:19 final size:19
Alignment explanation
Indices: 9995--10043 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
9985 GGTTACCAGA
*
9995 TTAGGGTTTGACTTTGGTT
1 TTAGGGTTTGACTTTAGTT
10014 TTAGGGTTTGACTTTAGTT
1 TTAGGGTTTGACTTTAGTT
*
10033 TTAAGGTTTGA
1 TTAGGGTTTGA
10044 GCCATTTGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.16, C:0.04, G:0.29, T:0.51
Consensus pattern (19 bp):
TTAGGGTTTGACTTTAGTT
Found at i:10147 original size:6 final size:6
Alignment explanation
Indices: 10136--10247 Score: 58
Period size: 6 Copynumber: 19.3 Consensus size: 6
10126 GAACATTATT
* * *
10136 AATTTA AATTTA GAA--TA ATTTTA AATTTA AGA-ATA AATTTA AACTTA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA A-ATTTA AATTTA AATTTA
* * * *
10183 AA-TTA TATTGA AATTTTA AA-ATA AATTTA AATTTA AA-ATA AATTTA
1 AATTTA AATTTA AA-TTTA AATTTA AATTTA AATTTA AATTTA AATTTA
** *
10229 ACCTTA AA-ATA AATTTA AA
1 AATTTA AATTTA AATTTA AA
10248 AAATTGGGTT
Statistics
Matches: 78, Mismatches: 18, Indels: 20
0.67 0.16 0.17
Matches are distributed among these distances:
4 1 0.01
5 19 0.24
6 50 0.64
7 8 0.10
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (6 bp):
AATTTA
Found at i:10170 original size:18 final size:17
Alignment explanation
Indices: 10136--10247 Score: 134
Period size: 17 Copynumber: 6.5 Consensus size: 17
10126 GAACATTATT
*
10136 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAATA
*
10153 ATTTTAAATTTAAGAATA
1 AATTTAAATTTAA-AATA
* *
10171 AATTTAAACTTAAATTA
1 AATTTAAATTTAAAATA
* *
10188 TATTGAAATTTTAAAATA
1 AATTTAAA-TTTAAAATA
10206 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
**
10223 AATTTAACCTTAAAATA
1 AATTTAAATTTAAAATA
10240 AATTTAAA
1 AATTTAAA
10248 AAATTGGGTT
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
17 51 0.65
18 28 0.35
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:10177 original size:35 final size:33
Alignment explanation
Indices: 10136--10247 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 33
10126 GAACATTATT
10136 AATTTAAATTTAGAATAATTTTAAATTTAAGAATA
1 AATTTAAATTTA-AATAATTTTAAATTTAA-AATA
* * *
10171 AATTTAAACTTAAATTATATTGAAATTTTAAAATA
1 AATTTAAATTTAAATAAT-TTTAAA-TTTAAAATA
* **
10206 AATTTAAATTTAAAATAAATTTAACCTTAAAATA
1 AATTTAAATTT-AAATAATTTTAAATTTAAAATA
10240 AATTTAAA
1 AATTTAAA
10248 AAATTGGGTT
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
34 21 0.32
35 34 0.52
36 10 0.15
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (33 bp):
AATTTAAATTTAAATAATTTTAAATTTAAAATA
Found at i:10875 original size:41 final size:43
Alignment explanation
Indices: 10781--10875 Score: 99
Period size: 43 Copynumber: 2.3 Consensus size: 43
10771 TATCTTACCT
* * *
10781 AAATATAATTTCGTTCTTAAAAAAAACTAATAAATTAAACCCA
1 AAATATATTTTCCTTCTTAAAAAAAACTAATAAATTAAACCAA
* *
10824 AAAT-TAATTTTCTCTTCTT-AAAAAAACT-CTAAATTAAA-TAA
1 AAATAT-ATTTTC-CTTCTTAAAAAAAACTAATAAATTAAACCAA
10865 AAATATATTTT
1 AAATATATTTT
10876 TTAAAAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
41 10 0.23
42 11 0.25
43 18 0.41
44 5 0.11
ACGTcount: A:0.51, C:0.12, G:0.01, T:0.37
Consensus pattern (43 bp):
AAATATATTTTCCTTCTTAAAAAAAACTAATAAATTAAACCAA
Found at i:11729 original size:33 final size:33
Alignment explanation
Indices: 11691--11756 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
11681 TTAAAAGTTA
*
11691 AATTTATTAAAAATTTT-AAATTAAAATTAAAAT
1 AATTTATT-AAAATTTTCAAATTAAAACTAAAAT
* *
11724 AATTTATTAGAATTTTCAAATTTAAACTAAAAT
1 AATTTATTAAAATTTTCAAATTAAAACTAAAAT
11757 GATAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 7 0.24
33 22 0.76
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (33 bp):
AATTTATTAAAATTTTCAAATTAAAACTAAAAT
Found at i:15177 original size:21 final size:22
Alignment explanation
Indices: 15138--15179 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
15128 ATTGTCGGTA
**
15138 AATTATTCGAGTTTGATTCGAT
1 AATTATTCGAGTTAAATTCGAT
15160 AATTA-TCGAGTTAAATTCGA
1 AATTATTCGAGTTAAATTCGA
15180 ATTTAGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (22 bp):
AATTATTCGAGTTAAATTCGAT
Found at i:17187 original size:6 final size:6
Alignment explanation
Indices: 17176--17201 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
17166 TTTAAAGGCT
17176 ATTTAA ATTTAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA AT
17202 AGGAACAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Done.