Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009770.1 Kokia drynarioides strain JFW-HI SEQ_124491, 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: 20492
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:472 original size:231 final size:235
Alignment explanation
Indices: 23--489 Score: 764
Period size: 231 Copynumber: 2.0 Consensus size: 235
13 ATATGCAATA
23 TGTTGACTGGTGGTGGCTCAATTGATCCACTTGGTCCTGAAAAGATAATAAAAAATCCATGAATG
1 TGTTGACTGGTGGTGGCTCAATTGATCCACTTGGTCCTGAAAAGATAATAAAAAATCCATGAATG
*
88 TATGATACACATATACATATACATATAGTAAACCAAGGCCAACACTTCATGCATCTCATGCATAT
66 TATGATACACATATACA-ATACATATAGTAAACCAAGGCCAACACTGCATGCATCTCATGCATAT
* * *
153 CTTCTCAAATAAGCAGATACACATTATTCATCTCCTTTTTTTTTAACACTGAATGAACCAAAACC
130 CTTCTCAAATAAGCAGATACACATTATTCATCTCCTGTTCTTGTAACACTGAATGAACCAAAACC
*
218 AGATAAAAGGCCAAGCTAACCTTCACCATGATGTCCAGTGG
195 AGATAAAAGGCCAAGCTAACCTTCACCATGATATCCAGTGG
*
259 TGTTGACTGGTGGTGGCTCAATTGATCCACTTGGTCCTGAAAAGATAATAAAGAATCCATGAATG
1 TGTTGACTGGTGGTGGCTCAATTGATCCACTTGGTCCTGAAAAGATAATAAAAAATCCATGAATG
* * * * *
324 TATGATATACATATGC-AT-GA-A-A-TAAACGAAGGCCAGCACTGCATGCATCTCATGCATATC
66 TATGATACACATATACAATACATATAGTAAACCAAGGCCAACACTGCATGCATCTCATGCATATC
*
384 TTCTCAAATAAAGCAGATACACATTATTCATCTCCTGTTCTTGTAACACTGAATGAACTAAAACC
131 TTCTCAAAT-AAGCAGATACACATTATTCATCTCCTGTTCTTGTAACACTGAATGAACCAAAACC
*
449 AGATAAAAGGCCAAGCTAACCTTCACCATGATATCTAGTGG
195 AGATAAAAGGCCAAGCTAACCTTCACCATGATATCCAGTGG
490 CGGTTTCCTG
Statistics
Matches: 217, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
230 44 0.20
231 91 0.42
232 1 0.00
233 1 0.00
234 2 0.01
236 78 0.36
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (235 bp):
TGTTGACTGGTGGTGGCTCAATTGATCCACTTGGTCCTGAAAAGATAATAAAAAATCCATGAATG
TATGATACACATATACAATACATATAGTAAACCAAGGCCAACACTGCATGCATCTCATGCATATC
TTCTCAAATAAGCAGATACACATTATTCATCTCCTGTTCTTGTAACACTGAATGAACCAAAACCA
GATAAAAGGCCAAGCTAACCTTCACCATGATATCCAGTGG
Found at i:3553 original size:36 final size:36
Alignment explanation
Indices: 3513--3581 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
3503 TCGAACTAAT
* *
3513 TGAAAATT-TGACTTAT-TTTATATTATTTATAATTTA
1 TGAAAATTAT-ACTTATATTT-TATAATATATAATTTA
3549 TGAAAATTATACTTATATTTTATAATATATAAT
1 TGAAAATTATACTTATATTTTATAATATATAAT
3582 AGATATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 25 0.86
37 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (36 bp):
TGAAAATTATACTTATATTTTATAATATATAATTTA
Found at i:11050 original size:20 final size:19
Alignment explanation
Indices: 11025--11062 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
11015 AATAATGTTT
11025 AAAATTCAAAATCTTTATAA
1 AAAATTCAAAAT-TTTATAA
*
11045 AAAATTCTAAATTTTATA
1 AAAATTCAAAATTTTATA
11063 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTCAAAATTTTATAA
Found at i:11086 original size:19 final size:19
Alignment explanation
Indices: 11064--11117 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
11054 AATTTTATAT
11064 TTTTAAAAAAATAATAAAA
1 TTTTAAAAAAATAATAAAA
* *
11083 TTTTTAAAAAAT-CTAAAA
1 TTTTAAAAAAATAATAAAA
*
11101 -TTTATATAAAATAATAA
1 TTTTA-AAAAAATAATAA
11118 TTTTGGAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 3 0.11
18 11 0.39
19 14 0.50
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
TTTTAAAAAAATAATAAAA
Found at i:11111 original size:18 final size:18
Alignment explanation
Indices: 11065--11112 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
11055 ATTTTATATT
*
11065 TTTA-AAAAAATAATAAAA
1 TTTATAAAAAAT-CTAAAA
*
11083 TTTTTAAAAAATCTAAAA
1 TTTATAAAAAATCTAAAA
*
11101 TTTATATAAAAT
1 TTTATAAAAAAT
11113 AATAATTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TTTATAAAAAATCTAAAA
Found at i:11277 original size:36 final size:36
Alignment explanation
Indices: 11237--11324 Score: 167
Period size: 36 Copynumber: 2.4 Consensus size: 36
11227 TTAAAGGATG
11237 ATATTTTAATTTTTTTAAATTCTTATTCAATTTTCA
1 ATATTTTAATTTTTTTAAATTCTTATTCAATTTTCA
*
11273 ATATTTTAATTTTTTTAAATTTTTATTCAATTTTCA
1 ATATTTTAATTTTTTTAAATTCTTATTCAATTTTCA
11309 ATATTTTAATTTTTTT
1 ATATTTTAATTTTTTT
11325 TCTCATTCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.65
Consensus pattern (36 bp):
ATATTTTAATTTTTTTAAATTCTTATTCAATTTTCA
Found at i:12425 original size:29 final size:30
Alignment explanation
Indices: 12368--12426 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
12358 TTTATAAATG
12368 AATTTCGATTTAATGTGTAATATAATACATA
1 AATTTCGATTTAA-GTGTAATATAATACATA
*
12399 AATTTTGATTTAA-TGTAAT-TATATACAT
1 AATTTCGATTTAAGTGTAATATA-ATACAT
12427 GAAACTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 2 0.08
29 12 0.46
31 12 0.46
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (30 bp):
AATTTCGATTTAAGTGTAATATAATACATA
Found at i:16905 original size:4 final size:4
Alignment explanation
Indices: 16889--16985 Score: 65
Period size: 4 Copynumber: 24.2 Consensus size: 4
16879 AAATAAACGG
* * * * *
16889 GAAA GAAA TAAA GAAA GGAA GGAA GAAG GAGAA GAAA GAAA G-AA GAAG
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA
* * * *
16937 GAGAA GAAA GAAA G-AA GAAG GAGAG GAAA GAAA G-AA GAAG GCAA GAAA
1 GA-AA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
16985 G
1 G
16986 GTAATGTGTT
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
3 9 0.12
4 54 0.74
5 10 0.14
ACGTcount: A:0.63, C:0.01, G:0.35, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:16933 original size:20 final size:20
Alignment explanation
Indices: 16899--16977 Score: 131
Period size: 20 Copynumber: 3.9 Consensus size: 20
16889 GAAAGAAATA
*
16899 AAGAAAGGAAGGAAGAAGGAG
1 AAGAAA-GAAAGAAGAAGGAG
16920 AAGAAAGAAAGAAGAAGGAG
1 AAGAAAGAAAGAAGAAGGAG
16940 AAGAAAGAAAGAAGAAGGAG
1 AAGAAAGAAAGAAGAAGGAG
*
16960 AGGAAAGAAAGAAGAAGG
1 AAGAAAGAAAGAAGAAGG
16978 CAAGAAAGGT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
20 50 0.89
21 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (20 bp):
AAGAAAGAAAGAAGAAGGAG
Found at i:20333 original size:21 final size:21
Alignment explanation
Indices: 20307--20349 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
20297 TAGGGTCCAT
* *
20307 TTGCCCTGGAGGAGTAGAGTA
1 TTGCCCAGGAGGAATAGAGTA
20328 TTGCCCAGGAGGAATAGAGTA
1 TTGCCCAGGAGGAATAGAGTA
20349 T
1 T
20350 CGCGATGGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (21 bp):
TTGCCCAGGAGGAATAGAGTA
Found at i:20422 original size:45 final size:45
Alignment explanation
Indices: 20355--20480 Score: 171
Period size: 45 Copynumber: 2.8 Consensus size: 45
20345 AGTATCGCGA
* * *
20355 TGGCTCGTCAAACTCAGCCTGATATCCTTTCCTTGAGTATTGCAG
1 TGGCTCGTCAAACTGAGGCTGATATCCTTGCCTTGAGTATTGCAG
* * * *
20400 TGGCTCGTTAAATTGAGGCTGATATCCTTGGCTTGAGTATTGCGG
1 TGGCTCGTCAAACTGAGGCTGATATCCTTGCCTTGAGTATTGCAG
* *
20445 TGGCTCGTCAAACTGAGGTTGATATCCTTGGCTTGA
1 TGGCTCGTCAAACTGAGGCTGATATCCTTGCCTTGA
20481 TGAGCTATGC
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (45 bp):
TGGCTCGTCAAACTGAGGCTGATATCCTTGCCTTGAGTATTGCAG
Done.