Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014526.1 Kokia drynarioides strain JFW-HI SEQ_129565, 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: 34846
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Warning! 122 characters in sequence are not A, C, G, or T
Found at i:8482 original size:34 final size:34
Alignment explanation
Indices: 8444--8509 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
8434 GTAAAAACAA
* * *
8444 CAATGATGGTGAAATTAAATGTTGTAACGATACG
1 CAATGATGATGAAATTAAATGCTATAACGATACG
* *
8478 CAATGGTGATGAGATTAAATGCTATAACGATA
1 CAATGATGATGAAATTAAATGCTATAACGATA
8510 TTGTAACATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (34 bp):
CAATGATGATGAAATTAAATGCTATAACGATACG
Found at i:14197 original size:28 final size:28
Alignment explanation
Indices: 14164--14274 Score: 123
Period size: 28 Copynumber: 3.7 Consensus size: 28
14154 ACCCAAATTA
*
14164 TGGTTTATTTACATATAATTGATTAAAT
1 TGGTTTATTTACCTATAATTGATTAAAT
**
14192 TGGTTTATTTACCTATAATTTTTTAAACTCAATT
1 TGGTTTATTTACCTATAATTGATT--A---AA-T
14226 ATGGTTTATTTACCTATAATTGATTAAAT
1 -TGGTTTATTTACCTATAATTGATTAAAT
*
14255 TGGTTTATTTATCTATAATT
1 TGGTTTATTTACCTATAATT
14275 TTTTAACTCA
Statistics
Matches: 70, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
28 40 0.57
29 1 0.01
30 3 0.04
33 3 0.04
34 1 0.01
35 22 0.31
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52
Consensus pattern (28 bp):
TGGTTTATTTACCTATAATTGATTAAAT
Found at i:14231 original size:63 final size:62
Alignment explanation
Indices: 14159--14298 Score: 246
Period size: 63 Copynumber: 2.3 Consensus size: 62
14149 ACTAAACCCA
14159 AATTATGGTTTATTTACATATAATTGATTAAATTGGTTTATTTACCTATAATTTTTTAAACTC
1 AATTATGGTTTATTTACATATAATTGATTAAATTGGTTTATTTACCTATAATTTTTT-AACTC
* *
14222 AATTATGGTTTATTTACCTATAATTGATTAAATTGGTTTATTTATCTATAATTTTTTAACTC
1 AATTATGGTTTATTTACATATAATTGATTAAATTGGTTTATTTACCTATAATTTTTTAACTC
14284 AATTATGGTTT-TTTA
1 AATTATGGTTTATTTA
14299 AATTTGATTG
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
61 4 0.05
62 16 0.21
63 55 0.73
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.53
Consensus pattern (62 bp):
AATTATGGTTTATTTACATATAATTGATTAAATTGGTTTATTTACCTATAATTTTTTAACTC
Found at i:14238 original size:35 final size:34
Alignment explanation
Indices: 14192--14298 Score: 129
Period size: 35 Copynumber: 3.3 Consensus size: 34
14182 TTGATTAAAT
14192 TGGTTTATTTACCTATAATTTTTTAAACTCAATTA
1 TGGTTTATTTACCTATAATTTTTT-AACTCAATTA
**
14227 TGGTTTATTTACCTATAATTGATT-A---AA-T-
1 TGGTTTATTTACCTATAATTTTTTAACTCAATTA
*
14255 TGGTTTATTTATCTATAATTTTTTAACTCAATTA
1 TGGTTTATTTACCTATAATTTTTTAACTCAATTA
14289 TGGTTT-TTTA
1 TGGTTTATTTA
14299 AATTTGATTG
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
28 21 0.34
29 2 0.03
30 2 0.03
32 2 0.03
33 6 0.10
34 6 0.10
35 22 0.36
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.54
Consensus pattern (34 bp):
TGGTTTATTTACCTATAATTTTTTAACTCAATTA
Found at i:17608 original size:21 final size:20
Alignment explanation
Indices: 17571--17624 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
17561 TTAAAACCCC
* *
17571 AAATTAAAAAAATATTATTT
1 AAATTAATAAAATATTACTT
*
17591 TAATTAATAAAATAATTACTT
1 AAATTAATAAAAT-ATTACTT
*
17612 AAATAAATAAAAT
1 AAATTAATAAAAT
17625 TAAAAGTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATTAATAAAATATTACTT
Found at i:17835 original size:58 final size:58
Alignment explanation
Indices: 17772--17915 Score: 152
Period size: 58 Copynumber: 2.5 Consensus size: 58
17762 ATCGAACAAA
* * *
17772 AAAAAAGATTAAGTACCAAATTAGGAAAAAA-GTCAAGTTCAAATACTAAACTGAACCC
1 AAAAAA-ATTAAGTACCAAATTAAGAAAAAACATCAAGTTCAAATACCAAACTGAACCC
* * * * *
17830 AAAAAAATTAAGTACTAACTTAAGAAAAAACATCAAGTTTAAATACCAAATTGAA--G
1 AAAAAAATTAAGTACCAAATTAAGAAAAAACATCAAGTTCAAATACCAAACTGAACCC
*
17886 AAAAACAATTTAAATACCAAATTAA-AAAAA
1 AAAAA-AA-TTAAGTACCAAATTAAGAAAAA
17916 TATAAAATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
56 5 0.07
57 28 0.39
58 39 0.54
ACGTcount: A:0.58, C:0.12, G:0.08, T:0.21
Consensus pattern (58 bp):
AAAAAAATTAAGTACCAAATTAAGAAAAAACATCAAGTTCAAATACCAAACTGAACCC
Found at i:17922 original size:7 final size:7
Alignment explanation
Indices: 17913--17947 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
17903 CAAATTAAAA
*
17913 AAATATA
1 AAATATT
17920 AAAT-TT
1 AAATATT
17926 AAATATT
1 AAATATT
17933 AAATATT
1 AAATATT
17940 AAATATT
1 AAATATT
17947 A
1 A
17948 TATTAAACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATATT
Found at i:17941 original size:14 final size:13
Alignment explanation
Indices: 17913--17947 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
17903 CAAATTAAAA
*
17913 AAATATAAAATTT
1 AAATATTAAATTT
17926 AAATATTAAATATT
1 AAATATTAAAT-TT
17940 AAATATTA
1 AAATATTA
17948 TATTAAACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATATTAAATTT
Found at i:20191 original size:24 final size:25
Alignment explanation
Indices: 20164--20218 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
20154 TAAAAATAAT
20164 TATATTAAAAAT-TTTATTAAATTA
1 TATATTAAAAATCTTTATTAAATTA
**
20188 TATATT-ATTATCTTTATTAAATTA
1 TATATTAAAAATCTTTATTAAATTA
20212 TAT-TTAA
1 TATATTAA
20219 TAATAATCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TATATTAAAAATCTTTATTAAATTA
Found at i:20774 original size:15 final size:16
Alignment explanation
Indices: 20746--20778 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
20736 GTAACCTTTT
20746 TTTTTACTTCATTTCC
1 TTTTTACTTCATTTCC
*
20762 TTTTTCCTT-ATTTCC
1 TTTTTACTTCATTTCC
20777 TT
1 TT
20779 CTTTTTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTACTTCATTTCC
Found at i:23221 original size:70 final size:67
Alignment explanation
Indices: 23128--23260 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 67
23118 CCAAATAAAA
* * **
23128 AAAAGGTAAAACTACGTCGTTTTGATAAATGTTTACCCTTTCTAAAGTTAAAATTCAAAACCATT
1 AAAAGGTAAAACTACGTCGTTTTGATAAATATTTACCC-AT-T-AAGTTAAAAGGCAAAACCATT
23193 AAGTT
63 AAGTT
* * *
23198 AAAAGGTAAAATTATGTCTTTTTGATAAATATTTACCCATTAAGTTAAAAGGCAAAACCATTA
1 AAAAGGTAAAACTACGTCGTTTTGATAAATATTTACCCATTAAGTTAAAAGGCAAAACCATTA
23261 TATTGTTTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 20 0.36
68 1 0.02
69 1 0.02
70 34 0.61
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (67 bp):
AAAAGGTAAAACTACGTCGTTTTGATAAATATTTACCCATTAAGTTAAAAGGCAAAACCATTAAG
TT
Found at i:24536 original size:16 final size:16
Alignment explanation
Indices: 24511--24544 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
24501 TTTTAGAGGA
*
24511 TTAAAAAAAATTAATT
1 TTAAAAAAAAATAATT
*
24527 TTAAATAAAAATAATT
1 TTAAAAAAAAATAATT
24543 TT
1 TT
24545 GGGGCTTGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAAAAAAAATAATT
Found at i:24903 original size:19 final size:19
Alignment explanation
Indices: 24867--24903 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
24857 AATGGAGGTT
*
24867 AATCAACAGTCAAGAATAC
1 AATCAACAGTAAAGAATAC
*
24886 AATCAACAGTAAATAATA
1 AATCAACAGTAAAGAATA
24904 TATAAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.16, G:0.08, T:0.19
Consensus pattern (19 bp):
AATCAACAGTAAAGAATAC
Found at i:29765 original size:60 final size:61
Alignment explanation
Indices: 29698--29848 Score: 162
Period size: 62 Copynumber: 2.5 Consensus size: 61
29688 GAAAAATTAG
* * * *
29698 TATATTATCATGAGATGAACATACTAATTGA-TA-AAATAATTTTTCGAACAATATATTGTA
1 TATATTATCATGAGATCAACATACTAATTGATTATAAATAATTTTT-AAACAATAGATTATA
** *
29758 TATATTATCATGAGATCTCCATACTAATTGATTTATCAATAATTTTTAAACAATAGATTATA
1 TATATTATCATGAGATCAACATACTAATTGA-TTATAAATAATTTTTAAACAATAGATTATA
* * * * *
29820 TATATTTTCTTAAAATCACCATACTAATT
1 TATATTATCATGAGATCAACATACTAATT
29849 TATAATGTAC
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
60 28 0.37
62 38 0.50
63 10 0.13
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (61 bp):
TATATTATCATGAGATCAACATACTAATTGATTATAAATAATTTTTAAACAATAGATTATA
Found at i:31878 original size:8 final size:8
Alignment explanation
Indices: 31843--31882 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
31833 GCTAATAAGA
31843 ATGTATGC
1 ATGTATGC
*
31851 ATGCATGC
1 ATGTATGC
*
31859 ATGCATGC
1 ATGTATGC
*
31867 ATGTATGT
1 ATGTATGC
31875 ATGTATGC
1 ATGTATGC
31883 TTGTTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (8 bp):
ATGTATGC
Found at i:32078 original size:8 final size:8
Alignment explanation
Indices: 32065--32095 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
32055 ATCTCATATG
*
32065 TGTATGTA
1 TGTATGCA
32073 TGTATGCA
1 TGTATGCA
32081 TGTATGCA
1 TGTATGCA
32089 TGTATGC
1 TGTATGC
32096 TTGTCTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.42
Consensus pattern (8 bp):
TGTATGCA
Done.