Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001114.1 Kokia drynarioides strain JFW-HI SEQ_112395, 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: 97424
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 90 characters in sequence are not A, C, G, or T
Found at i:902 original size:2 final size:2
Alignment explanation
Indices: 895--924 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
885 TACTCTCACC
895 AT AT 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 AT AT
925 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13944 original size:13 final size:14
Alignment explanation
Indices: 13921--13949 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
13911 AGAATTTGAA
13921 TAAAAATATAAATT
1 TAAAAATATAAATT
13935 TAAAAA-ATAAATT
1 TAAAAATATAAATT
13948 TA
1 TA
13950 GGTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAAAATATAAATT
Found at i:14078 original size:11 final size:11
Alignment explanation
Indices: 14055--14088 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
14045 CTTGTTGTTT
14055 TCATTGTTTTTG
1 TCATTG-TTTTG
*
14067 TTATTGTTTTG
1 TCATTGTTTTG
14078 TCATTGTTTTG
1 TCATTGTTTTG
14089 GTGTCGTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.09, C:0.06, G:0.18, T:0.68
Consensus pattern (11 bp):
TCATTGTTTTG
Found at i:14582 original size:213 final size:212
Alignment explanation
Indices: 14206--14612 Score: 554
Period size: 213 Copynumber: 1.9 Consensus size: 212
14196 TAAGTTGCAC
* *
14206 TTATCTTAATATTATTTAAGTATAAATAATTTTTTTAATTTATTTTCAAAGCTTTGGGGAACATT
1 TTATCTTAATATTAATTAAGTATAAATAATTTTTTTAATTTATTTTCAAA-CTTTGGGAAACATT
* *
14271 TATTTTAATGCTTTAGTGTACTTGATGTATTATATTTTTTTAAATTTATTTTTATATAAAAATTT
65 TATTTTAATGCTTTAGTGTAATAGATGTATTATATTTTTTTAAATTTATTTTTATATAAAAATTT
** *
14336 AATATGATTTGACCAAGCAGAACTCGGATTTTAGCATTTTTATCTGAGCCGAATTTGAGTAAAAA
130 AATATGATCGGACCAAGCAGAACTCGAATTTTAGCATTTTTATCTGAGCCGAATTTGAGTAAAAA
14401 ATTAGGCTCATTTTAGGT
195 ATTAGGCTCATTTTAGGT
* * *
14419 TTATCTTAGTGTTAATTAAGTATAAATAATTTTTTTAATTTATTTTC-AA-TTTGTTGGAAACTT
1 TTATCTTAATATTAATTAAGTATAAATAATTTTTTTAATTTATTTTCAAACTTTG--GGAAACAT
* * *
14482 TTATTTTACTGTTTTAGTGTAATA-AGTGTATTATA-TTTTTTAAATTTGTTTTTATATAAAAAA
64 TTATTTTAATGCTTTAGTGTAATAGA-TGTATTATATTTTTTTAAATTTATTTTTATAT--AAAA
* * ** *
14545 ATTTAATATGATCGGACCAAGCCA-AGCTCGAATTTTAGCATTTTTATTTGAGGTGAATTTTAGT
126 ATTTAATATGATCGGACCAAG-CAGAACTCGAATTTTAGCATTTTTATCTGAGCCGAATTTGAGT
14609 AAAA
190 AAAA
14613 TTTTAAGTTC
Statistics
Matches: 170, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
210 4 0.02
211 22 0.13
212 37 0.22
213 105 0.62
214 2 0.01
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (212 bp):
TTATCTTAATATTAATTAAGTATAAATAATTTTTTTAATTTATTTTCAAACTTTGGGAAACATTT
ATTTTAATGCTTTAGTGTAATAGATGTATTATATTTTTTTAAATTTATTTTTATATAAAAATTTA
ATATGATCGGACCAAGCAGAACTCGAATTTTAGCATTTTTATCTGAGCCGAATTTGAGTAAAAAA
TTAGGCTCATTTTAGGT
Found at i:15965 original size:19 final size:16
Alignment explanation
Indices: 15937--15976 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 16
15927 GTGCTCCCCA
15937 AATTAATTAGTTCGTTT
1 AATTAATTAGTT-GTTT
15954 GAATTGAATTAGTTGTTT
1 -AATT-AATTAGTTGTTT
15972 AATTA
1 AATTA
15977 TTTATTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 1 0.05
17 4 0.19
18 8 0.38
19 8 0.38
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.50
Consensus pattern (16 bp):
AATTAATTAGTTGTTT
Found at i:16280 original size:2 final size:2
Alignment explanation
Indices: 16273--16300 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16263 AAATTTGACA
16273 AT 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 AT
16301 CTAAAACACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35320 original size:18 final size:16
Alignment explanation
Indices: 35289--35332 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
35279 GGTTTAGAGT
*
35289 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
35306 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
35320 TTAAAAATTTATT
1 TTAAAAATTTATT
35333 CTCATTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:49531 original size:7 final size:7
Alignment explanation
Indices: 49519--49551 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
49509 ATAACAAACA
49519 TAAACCT
1 TAAACCT
49526 TAAACCT
1 TAAACCT
49533 TAAACCT
1 TAAACCT
*
49540 TAAACCC
1 TAAACCT
49547 TAAAC
1 TAAAC
49552 TTGCAACGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAACCT
Found at i:50252 original size:3 final size:3
Alignment explanation
Indices: 50244--50273 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
50234 GCTACTCAGG
50244 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
50274 GACAATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:50877 original size:80 final size:83
Alignment explanation
Indices: 50724--50902 Score: 195
Period size: 81 Copynumber: 2.2 Consensus size: 83
50714 CTTTAAAGTT
* * * * * *
50724 TTTAAAAGAACAAAATCATAATTTTATCATTTTAGTGAGCCAAACTACAATTTTACCATCGTAAT
1 TTTAAAAGGACTAGATCATAATTTTATCATTTTAGAGAGCAAAAATACAATTTTACCATCGTAAT
*
50789 AGCTTATAACTTTA-CAA
66 AACTTATAACTTTACCAA
* * * * * *
50806 -TTAGAAGGACTAGATCATAA-TTTATCATTTTGGAAGAGCAAAAATGCAATTTTATCGT-GTAT
1 TTTAAAAGGACTAGATCATAATTTTATCATTTTAG-AGAGCAAAAATACAATTTTACCATCGTAA
50868 TAACTTATAACTTTACCAA
65 TAACTTATAACTTTACCAA
50887 TTTTAAAAGGACTAGA
1 -TTTAAAAGGACTAGA
50903 GTACAACTTT
Statistics
Matches: 79, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
80 29 0.37
81 37 0.47
83 13 0.16
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.35
Consensus pattern (83 bp):
TTTAAAAGGACTAGATCATAATTTTATCATTTTAGAGAGCAAAAATACAATTTTACCATCGTAAT
AACTTATAACTTTACCAA
Found at i:54391 original size:29 final size:29
Alignment explanation
Indices: 54359--54418 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
54349 ATTGAGTGAT
*
54359 CATTTTGTAACTTTTCATAATTGGGCGAC
1 CATTTTATAACTTTTCATAATTGGGCGAC
* * *
54388 CATTTTATAACTTTTTATAGTTGGGTGAC
1 CATTTTATAACTTTTCATAATTGGGCGAC
54417 CA
1 CA
54419 AAAAAGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (29 bp):
CATTTTATAACTTTTCATAATTGGGCGAC
Found at i:63565 original size:22 final size:21
Alignment explanation
Indices: 63509--63565 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
63499 AACTTTTTTC
* *
63509 ATTAATTTTATATAATTATTGTT
1 ATTAATTTT-TA-AAATATAGTT
*
63532 ATTATTTTTTAAAATATAGTT
1 ATTAATTTTTAAAATATAGTT
63553 ATATAATTTTTAA
1 AT-TAATTTTTAA
63566 GAAATTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 10 0.34
22 11 0.38
23 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
ATTAATTTTTAAAATATAGTT
Found at i:78904 original size:2 final size:2
Alignment explanation
Indices: 78897--78928 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
78887 AAAATCCCAA
78897 AT AT AT 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 AT AT AT
78929 GCAACAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84131 original size:2 final size:2
Alignment explanation
Indices: 84126--84162 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
84116 TTTTTTAAAT
84126 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
84163 TTAAAATGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:87415 original size:2 final size:2
Alignment explanation
Indices: 87408--87442 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
87398 CAAAGAGACC
87408 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
87443 TAAAAGGATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:91988 original size:29 final size:29
Alignment explanation
Indices: 91956--92022 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
91946 TTGAAATTTG
* * *
91956 GATTAATTTAATTATTTTCAATAATTCA-A
1 GATTAATTTAATCAATTT-AATAATACAGA
* *
91985 GATTAAATTAATCAATTTAATAATAGAGA
1 GATTAATTTAATCAATTTAATAATACAGA
92014 GATTAATTT
1 GATTAATTT
92023 GATTTGATCC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 7 0.23
29 24 0.77
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.43
Consensus pattern (29 bp):
GATTAATTTAATCAATTTAATAATACAGA
Done.