Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004035.1 Kokia drynarioides strain JFW-HI SEQ_117171, 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: 50206
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 42 characters in sequence are not A, C, G, or T
Found at i:246 original size:11 final size:10
Alignment explanation
Indices: 214--407 Score: 69
Period size: 10 Copynumber: 20.1 Consensus size: 10
204 ATTTTAATCA
214 ATAAAAGTTAT
1 ATAAAA-TTAT
225 A-AAAA-TAT
1 ATAAAATTAT
233 ATAGAAATTAT
1 ATA-AAATTAT
244 ATAAAATT-T
1 ATAAAATTAT
**
253 ATTAAAAAAAT
1 A-TAAAATTAT
* * *
264 AAAAAATAAAAG
1 ATAAAAT--TAT
276 ATAAAAGTTAT
1 ATAAAA-TTAT
*
287 AGAAAATTAT
1 ATAAAATTAT
*
297 -TAAAAATAT
1 ATAAAATTAT
*
306 ATAAAAATAT
1 ATAAAATTAT
316 ATTATAAA--AT
1 A-TA-AAATTAT
* *
326 AT-AATTTTT
1 ATAAAATTAT
335 A-AGAAATTA-
1 ATA-AAATTAT
*
344 A-GAAATTAT
1 ATAAAATTAT
353 A-AAAA-TAT
1 ATAAAATTAT
*
361 ATAAATTTAT
1 ATAAAATTAT
371 -TAAAA-TAT
1 ATAAAATTAT
379 A-AAAATTAT
1 ATAAAATTAT
*
388 AGAAAATTAT
1 ATAAAATTAT
*
398 -TAAAAATAT
1 ATAAAATTAT
407 A
1 A
408 AAGTTTCAGT
Statistics
Matches: 140, Mismatches: 21, Indels: 45
0.68 0.10 0.22
Matches are distributed among these distances:
7 2 0.01
8 21 0.15
9 36 0.26
10 53 0.38
11 17 0.12
12 10 0.07
13 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (10 bp):
ATAAAATTAT
Found at i:323 original size:43 final size:42
Alignment explanation
Indices: 222--325 Score: 115
Period size: 43 Copynumber: 2.5 Consensus size: 42
212 CAATAAAAGT
* *
222 TATAAAAATATATA-GAAATTATATAAAATTTATTAAAAAAA
1 TATAAAAATATATATAAAATTATAGAAAATTTATTAAAAAAA
* * *
263 TA-AAAAATAAAAGATAAAAGTTATAGAAAA-TTATTAAAAATA
1 TATAAAAAT-ATATATAAAA-TTATAGAAAATTTATTAAAAAAA
305 TATAAAAATATATTATAAAAT
1 TATAAAAATATA-TATAAAAT
326 ATAATTTTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
40 6 0.12
41 5 0.10
42 19 0.37
43 21 0.41
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (42 bp):
TATAAAAATATATATAAAATTATAGAAAATTTATTAAAAAAA
Found at i:375 original size:18 final size:18
Alignment explanation
Indices: 299--404 Score: 62
Period size: 18 Copynumber: 5.8 Consensus size: 18
289 AAAATTATTA
*
299 AAAATATATAAAAATATATT
1 AAAA-ATATAAAAATTTA-T
*
319 ATAAAATAT---AATTTTT
1 A-AAAATATAAAAATTTAT
335 AAGAAAT-TAAGAAA-TTAT
1 AA-AAATATAA-AAATTTAT
*
353 AAAAATATATAAATTTAT
1 AAAAATATAAAAATTTAT
*
371 TAAAATATAAAAA-TTAT
1 AAAAATATAAAAATTTAT
388 AGAAAATTATTAAAAAT
1 A-AAAA-TA-TAAAAAT
405 ATAAAGTTTC
Statistics
Matches: 67, Mismatches: 7, Indels: 23
0.69 0.07 0.24
Matches are distributed among these distances:
15 2 0.03
16 6 0.09
17 15 0.22
18 26 0.39
19 4 0.06
20 11 0.16
21 3 0.04
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AAAAATATAAAAATTTAT
Found at i:395 original size:53 final size:55
Alignment explanation
Indices: 216--409 Score: 141
Period size: 62 Copynumber: 3.4 Consensus size: 55
206 TTTAATCAAT
* * *
216 AAAAGTTATA-AAAATATATAGAAATTATATAAAATTTATTAAAAAAATAAAAAATAAAAG
1 AAAA-TTATAGAAAAT-TATA-AAAATATATAAAATTTATT--AAAAAT-AAAAATTATAG
* * * *
276 ATAAAAGTTATAGAAAATTATTAAAAATATATAAAAATATATTATAAAATATAATTTTTA-
1 --AAAA-TTATAGAAAATTA-TAAAAATATAT-AAAATTTATTA-AAAATAAAAATTATAG
336 AGAAATTA-AG-AAATTATAAAAATATAT-AAATTTATTAAAATATAAAAATTATAG
1 A-AAATTATAGAAAATTATAAAAATATATAAAATTTATTAAAA-ATAAAAATTATAG
390 AAAATTATTA-AAAA-TATAAA
1 AAAATTA-TAGAAAATTATAAA
410 GTTTCAGTAA
Statistics
Matches: 111, Mismatches: 11, Indels: 28
0.74 0.07 0.19
Matches are distributed among these distances:
52 3 0.03
53 24 0.22
54 7 0.06
55 15 0.14
56 6 0.05
57 2 0.02
58 4 0.04
59 3 0.03
61 6 0.05
62 25 0.23
63 16 0.14
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (55 bp):
AAAATTATAGAAAATTATAAAAATATATAAAATTTATTAAAAATAAAAATTATAG
Found at i:864 original size:75 final size:75
Alignment explanation
Indices: 738--970 Score: 344
Period size: 82 Copynumber: 3.0 Consensus size: 75
728 TTGAGGTCTG
*
738 GCTAGCTTCCTATCGAGTGAAGCTTTTGAAAACTTTTCCCAAAGAAA-TTGCCCACAACAAATAA
1 GCTAGCTTCCTATCGAGTGAAACTTTTGAAAACTTTTCCCAAA-AAAGTTGCCCACAACAAATAA
802 AAATAGTAATA
65 AAATAGTAATA
*
813 GCTAGCTTCCTATCAAGTGAAACTTTTGAAAAC-TTTCTCCAAAAAAGTTGCCCACAACAAACAA
1 GCTAGCTTCCTATCGAGTGAAACTTTTGAAAACTTTTC-CCAAAAAAGTTG--C-C--C--ACAA
877 CAAATAAAAATAGTAATA
58 CAAATAAAAATAGTAATA
*
895 GGTAGCTTCCTATCGAGTGAAACTTTTGAAAACTTTTCCCAAAAAAGTTGCCCACAACAAATAAA
1 GCTAGCTTCCTATCGAGTGAAACTTTTGAAAACTTTTCCCAAAAAAGTTGCCCACAACAAATAAA
960 AATAGTAATA
66 AATAGTAATA
970 G
1 G
971 TCGAACGTGA
Statistics
Matches: 144, Mismatches: 4, Indels: 20
0.86 0.02 0.12
Matches are distributed among these distances:
74 7 0.05
75 62 0.43
77 2 0.01
78 1 0.01
79 1 0.01
80 2 0.01
82 65 0.45
83 4 0.03
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (75 bp):
GCTAGCTTCCTATCGAGTGAAACTTTTGAAAACTTTTCCCAAAAAAGTTGCCCACAACAAATAAA
AATAGTAATA
Found at i:2861 original size:16 final size:16
Alignment explanation
Indices: 2827--2872 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
2817 AAAAAACAAA
* *
2827 AGAAAAGG-AGAATAT
1 AGAAAAGGAAGAAAAG
2842 AGAAAAGGAAGAAAAG
1 AGAAAAGGAAGAAAAG
2858 AGAAAAGGGAAGAAA
1 AGAAAA-GGAAGAAA
2873 CAAAATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 8 0.30
16 11 0.41
17 8 0.30
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.04
Consensus pattern (16 bp):
AGAAAAGGAAGAAAAG
Found at i:5573 original size:17 final size:17
Alignment explanation
Indices: 5551--5584 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5541 GAAAAAATTC
*
5551 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
5568 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
5585 TCATAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:8210 original size:26 final size:26
Alignment explanation
Indices: 8155--8230 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
8145 GCTAAACCTC
**
8155 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
8181 ATTAAATAAATTCAAATTTAAATAGA
1 ATTAAATAAATTCAAACATAAAAAGA
* *
8207 ATTAATTCCAAATTCAATCATAAA
1 ATTAAAT--AAATTCAAACATAAA
8231 CTTAATTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 27 0.69
28 12 0.31
ACGTcount: A:0.57, C:0.09, G:0.01, T:0.33
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:11034 original size:26 final size:26
Alignment explanation
Indices: 11005--11056 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
10995 TTTTGCTAAC
* * *
11005 CTTTTGTTTCCTTTTCTTCTTCAAAA
1 CTTTTGCTTCATTTCCTTCTTCAAAA
*
11031 CTTTTGCTTCATTTCCTTTTTCAAAA
1 CTTTTGCTTCATTTCCTTCTTCAAAA
11057 ATTTGCTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.17, C:0.23, G:0.04, T:0.56
Consensus pattern (26 bp):
CTTTTGCTTCATTTCCTTCTTCAAAA
Found at i:26352 original size:23 final size:23
Alignment explanation
Indices: 26325--26408 Score: 78
Period size: 23 Copynumber: 3.4 Consensus size: 23
26315 AACTTGTTTC
*
26325 CTTCTCTTTTGCTGGAAATTTGT
1 CTTCTCTTTTGCTAGAAATTTGT
* * *
26348 CTTCTCATTTGATAGAAATGCATCTGC
1 CTTCTCTTTTGCTAGAAAT---T-TGT
*
26375 CTTCTCTTTTGCTTGAAATTTGT
1 CTTCTCTTTTGCTAGAAATTTGT
26398 CTTCTCATTTT
1 CTTCTC-TTTT
26409 CAGACTTGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
23 24 0.50
24 5 0.10
26 1 0.02
27 18 0.38
ACGTcount: A:0.17, C:0.20, G:0.13, T:0.50
Consensus pattern (23 bp):
CTTCTCTTTTGCTAGAAATTTGT
Found at i:32064 original size:2 final size:2
Alignment explanation
Indices: 32057--32082 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
32047 AAATAAAAAC
32057 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
32083 AATGAGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:37058 original size:33 final size:33
Alignment explanation
Indices: 37016--37083 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
37006 CAATGTATAA
*
37016 CATTAACAACATATATAATTGTTCAAACCCGAC
1 CATTAACAACATATATAAGTGTTCAAACCCGAC
37049 CATTAACAACATATATAAGTGTTCAAACCCGAC
1 CATTAACAACATATATAAGTGTTCAAACCCGAC
37082 CA
1 CA
37084 AACAAGAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.25
Consensus pattern (33 bp):
CATTAACAACATATATAAGTGTTCAAACCCGAC
Found at i:43423 original size:19 final size:20
Alignment explanation
Indices: 43385--43423 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
43375 TATATGTCAT
*
43385 TTTAAAAAAATAATTTAAAA
1 TTTAAAAAAATAATTCAAAA
*
43405 TTTATAAAAAT-ATTCAAAA
1 TTTAAAAAAATAATTCAAAA
43424 ATAGAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
TTTAAAAAAATAATTCAAAA
Found at i:44618 original size:3 final size:3
Alignment explanation
Indices: 44612--44638 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
44602 CTCTTCTTTT
44612 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
44639 GTGTTAGGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:50129 original size:23 final size:23
Alignment explanation
Indices: 50103--50206 Score: 118
Period size: 23 Copynumber: 4.4 Consensus size: 23
50093 AGTGCTGGGC
*
50103 AACAGAGAGCACACACAGTACTA
1 AACAGAGAGCACACAAAGTACTA
*
50126 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACAAAGTACTA
** *
50149 GTCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTACTA
* *
50172 ATCAGAGAGCACACACAAGTGCTAA
1 AACAGAGAGCACACA-AAGTACT-A
50197 TAACAGAGAG
1 -AACAGAGAG
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
23 54 0.77
24 7 0.10
25 1 0.01
26 8 0.11
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTACTA
Done.