Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004819.1 Kokia drynarioides strain JFW-HI SEQ_118453, 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: 22757
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1883 original size:18 final size:18
Alignment explanation
Indices: 1862--1909 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1852 AAATTTTTAG
1862 AATTTTTAAAAATATATA
1 AATTTTTAAAAATATATA
* ** *
1880 AATTTTGAAATTTTTATA
1 AATTTTTAAAAATATATA
1898 AATATTTTAAAA
1 AAT-TTTTAAAA
1910 TTTGAAAATT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
AATTTTTAAAAATATATA
Found at i:1894 original size:27 final size:27
Alignment explanation
Indices: 1851--1916 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
1841 TATATTTTTT
*
1851 TAAATTTTTAGAATTTTTAAAAATA-TA
1 TAAATTTTGA-AATTTTTAAAAATATTA
* *
1878 TAAATTTTGAAATTTTTATAAATATTT
1 TAAATTTTGAAATTTTTAAAAATATTA
*
1905 TAAAATTTGAAA
1 TAAATTTTGAAA
1917 ATTATTTTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 13 0.38
27 21 0.62
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (27 bp):
TAAATTTTGAAATTTTTAAAAATATTA
Found at i:2172 original size:23 final size:23
Alignment explanation
Indices: 2119--2172 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
2109 ATATTATATT
2119 ATTTCAATTATAATATGCTTTTGA
1 ATTT-AATTATAATATGCTTTTGA
** ** *
2143 AAGTAATTATAATATTTTTTTTA
1 ATTTAATTATAATATGCTTTTGA
2166 ATTTAAT
1 ATTTAAT
2173 AAGTTTTGTA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (23 bp):
ATTTAATTATAATATGCTTTTGA
Found at i:3592 original size:20 final size:20
Alignment explanation
Indices: 3569--3607 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3559 TTTTAAAATA
*
3569 TATATAAATTTTGAAATTTT
1 TATATAAATTTTAAAATTTT
*
3589 TATATATATTTTAAAATTT
1 TATATAAATTTTAAAATTT
3608 GAAAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TATATAAATTTTAAAATTTT
Found at i:3595 original size:63 final size:62
Alignment explanation
Indices: 3486--3604 Score: 145
Period size: 63 Copynumber: 1.9 Consensus size: 62
3476 ATTTAGGCCC
* *
3486 AAAATTATTATTTTAAAATATTTTCAAAATTTTAACTTTATTTATATATATTTAAAAAAAATTT
1 AAAATTATTATTTTAAAATATTAT-AAAATTTTAAATTTATTTATATAT-TTTAAAAAAAATTT
*
3550 AAAATTCTT-TTTTAAAATA-TATATAAATTTTGAAATTT-TTATATATATTTTAAAA
1 AAAATTATTATTTTAAAATATTATA-AAATTTT-AAATTTATT-TATATATTTTAAAA
3605 TTTGAAAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
61 1 0.02
62 18 0.37
63 22 0.45
64 8 0.16
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (62 bp):
AAAATTATTATTTTAAAATATTATAAAATTTTAAATTTATTTATATATTTTAAAAAAAATTT
Found at i:7328 original size:6 final size:6
Alignment explanation
Indices: 7309--7385 Score: 61
Period size: 6 Copynumber: 12.8 Consensus size: 6
7299 TAAAATTAGG
** **
7309 TTTAAA -TT-AA TTTAAA TTTATTT TTTAAA TTTAAA TTTATCTT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTA--AA TTTAAA
*
7358 TTTAAA TTT-AC TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
7386 TCAAATTTGA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
4 2 0.04
5 8 0.15
6 37 0.67
7 4 0.07
8 4 0.07
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:7355 original size:20 final size:20
Alignment explanation
Indices: 7317--7384 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
7307 GGTTTAAATT
7317 AATTTAAATTTAT-TTTTTA
1 AATTTAAATTTATCTTTTTA
7336 AATTTAAATTTATCTTTTTA
1 AATTTAAATTTATCTTTTTA
7356 AATTTAAATTTA-C--TTTA
1 AATTTAAATTTATCTTTTTA
7373 AATTTAAATTTA
1 AATTTAAATTTA
7385 ATCAAATTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.33
19 14 0.29
20 18 0.38
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTTAAATTTATCTTTTTA
Found at i:8139 original size:9 final size:9
Alignment explanation
Indices: 8127--8162 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
8117 ATGATGGTAA
8127 TAATAATAT
1 TAATAATAT
*
8136 TAATAATAA
1 TAATAATAT
8145 TAATAATAT
1 TAATAATAT
*
8154 TACTAATAT
1 TAATAATAT
8163 CATTAATAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (9 bp):
TAATAATAT
Found at i:9314 original size:29 final size:29
Alignment explanation
Indices: 9282--9560 Score: 325
Period size: 29 Copynumber: 9.5 Consensus size: 29
9272 CTAAACTGTT
9282 CAAAAATTCCATTTTTACCCTCAAACTTC
1 CAAAAATTCCATTTTTACCCTCAAACTTC
* *
9311 CAAAAATTCCA-TTTTAACTTCAAAACTTC
1 CAAAAATTCCATTTTTACCCTC-AAACTTC
*
9340 CAAAAATTCCATTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCCTCAAACTTC
9369 CAAAAATTCCATTTTTGA-CCTCGAAACTTC
1 CAAAAATTCCATTTTT-ACCCTC-AAACTTC
*
9399 CAAAAATTCCATTTTGACCC-CGAAACTTC
1 CAAAAATTCCATTTTTACCCTC-AAACTTC
*
9428 CAAAAATTCCATTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCCTCAAACTTC
*
9457 CAAAAATTCCATTTTTAACCCTAAAACTTC
1 CAAAAATTCCATTTTT-ACCCTCAAACTTC
* *
9487 CAAAAATTCCATTTTAAACCC-CGAA-TATC
1 CAAAAATTCCATTTT-TACCCTCAAACT-TC
* * **
9516 TAAAAATTCCATTTTTAACCTCGAATTTTC
1 CAAAAATTCCATTTTTACCCTC-AAACTTC
*
9546 CCAAAATTACCATTT
1 CAAAAATT-CCATTT
9561 CACCCATGAA
Statistics
Matches: 216, Mismatches: 21, Indels: 24
0.83 0.08 0.09
Matches are distributed among these distances:
28 12 0.06
29 125 0.58
30 72 0.33
31 7 0.03
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCTCAAACTTC
Found at i:9426 original size:59 final size:59
Alignment explanation
Indices: 9282--9560 Score: 347
Period size: 59 Copynumber: 4.7 Consensus size: 59
9272 CTAAACTGTT
* * *
9282 CAAAAATTCCATTTTTACCCTC-AAACTTCCAAAAATTCCATTTTAACTTCAAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTTACCTCGAAACTTC
9340 CAAAAATTCCATTTTTACCCTCG-AACTTCCAAAAATTCCATTTTTGACCTCGAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTT-ACCTCGAAACTTC
*
9399 CAAAAATTCCATTTTGACCC-CGAAACTTCCAAAAATTCCATTTTTACCCTCG-AACTTC
1 CAAAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTTA-CCTCGAAACTTC
* * *
9457 CAAAAATTCCATTTTTAACCCT-AAAACTTCCAAAAATTCCATTTTAAACCCCG-AA-TATC
1 CAAAAATTCCATTTTT-ACCCTCGAAACTTCCAAAAATTCCATTTT-TACCTCGAAACT-TC
* * ** *
9516 TAAAAATTCCATTTTTAACCTCGAATTTTCCCAAAATTACCATTT
1 CAAAAATTCCATTTTTACCCTCGAAACTTCCAAAAATT-CCATTT
9561 CACCCATGAA
Statistics
Matches: 197, Mismatches: 14, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
58 72 0.37
59 118 0.60
60 7 0.04
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (59 bp):
CAAAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTTACCTCGAAACTTC
Found at i:9430 original size:88 final size:86
Alignment explanation
Indices: 9282--9560 Score: 382
Period size: 88 Copynumber: 3.2 Consensus size: 86
9272 CTAAACTGTT
** *
9282 CAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTAACTTCAAAACTTCCAAAAAT
1 CAAAAATTCCATTTTTA-CCTCAAACTTCCAAAAATTCCATTTTAACCCCGAAACTTCCAAAAAT
9347 TCCATTTTTACCCTCGAACTTC
65 TCCATTTTTACCCTCGAACTTC
*
9369 CAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTGACCCCGAAACTTCCAAAAA
1 CAAAAATTCCATTTTT-ACCTC-AAACTTCCAAAAATTCCATTTTAACCCCGAAACTTCCAAAAA
9434 TTCCATTTTTACCCTCGAACTTC
64 TTCCATTTTTACCCTCGAACTTC
* *
9457 CAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTAAACCCCG-AA-TATCTAAA
1 CAAAAATTCCATTTTT-A-CCTCAAACTTCCAAAAATTCCATTTT-AACCCCGAAACT-TCCAAA
* *
9520 AATTCCATTTTTAACCTCGAATTTTC
62 AATTCCATTTTTACCCTCGAA-CTTC
*
9546 CCAAAATTACCATTT
1 CAAAAATT-CCATTT
9561 CACCCATGAA
Statistics
Matches: 174, Mismatches: 11, Indels: 11
0.89 0.06 0.06
Matches are distributed among these distances:
87 21 0.12
88 128 0.74
89 19 0.11
90 6 0.03
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (86 bp):
CAAAAATTCCATTTTTACCTCAAACTTCCAAAAATTCCATTTTAACCCCGAAACTTCCAAAAATT
CCATTTTTACCCTCGAACTTC
Found at i:13563 original size:47 final size:47
Alignment explanation
Indices: 13502--13637 Score: 148
Period size: 47 Copynumber: 2.9 Consensus size: 47
13492 ATGACTGCTG
* *
13502 ACTAAAATACGTTGTGGATAAACCAATGGTCGAGCAAATGAATACCA
1 ACTAAAATACGTTGTGGATAAACCATTGGTCGAGCAGATGAATACCA
* * * * * *
13549 ACTATAATATGTTGT-GATAAAATCATTGGTCGAGCAGATGACTGCCG
1 ACTAAAATACGTTGTGGAT-AAACCATTGGTCGAGCAGATGAATACCA
* * * *
13596 ACTAGAATACATTGTGGAAAAACCATTAGTCGAGCAGATGAA
1 ACTAAAATACGTTGTGGATAAACCATTGGTCGAGCAGATGAA
13638 CTATTGACTA
Statistics
Matches: 72, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
46 3 0.04
47 67 0.93
48 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (47 bp):
ACTAAAATACGTTGTGGATAAACCATTGGTCGAGCAGATGAATACCA
Found at i:13814 original size:34 final size:34
Alignment explanation
Indices: 13759--13825 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
13749 GGTAGCATTC
* *
13759 AATATGCTTATAACATATCAACTCAGTATCAAAT
1 AATATGCTTATAACAGATCAACTCAGTAGCAAAT
* * *
13793 AATATGCTTATAATAGGTCAACTTAGTAGCAAA
1 AATATGCTTATAACAGATCAACTCAGTAGCAAA
13826 AGTCATGCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.31
Consensus pattern (34 bp):
AATATGCTTATAACAGATCAACTCAGTAGCAAAT
Found at i:16528 original size:2 final size:2
Alignment explanation
Indices: 16521--16581 Score: 90
Period size: 2 Copynumber: 31.5 Consensus size: 2
16511 GATCAAAGTA
*
16521 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
16563 AT AT AT -T AT AA AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT A
16582 AGTGTTAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.