Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006022.1 Kokia drynarioides strain JFW-HI SEQ_120466, 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: 60066
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Warning! 63 characters in sequence are not A, C, G, or T
Found at i:332 original size:15 final size:15
Alignment explanation
Indices: 314--367 Score: 74
Period size: 15 Copynumber: 3.6 Consensus size: 15
304 TTTTGGGTAG
*
314 TTTGTAATTGGGTCA
1 TTTGTAATTGGGCCA
329 TTTGT-ATTCGGGCCA
1 TTTGTAATT-GGGCCA
*
344 TCTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
359 TTTGTAATT
1 TTTGTAATT
368 AGACTTTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.09
15 28 0.82
16 3 0.09
ACGTcount: A:0.19, C:0.13, G:0.24, T:0.44
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:410 original size:17 final size:16
Alignment explanation
Indices: 388--449 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
378 TTGGACTTTC
388 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
*
405 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTTAAA
* *
422 TAAACTTAAATTTAAA
1 TAAATTTAATTTTAAA
* *
438 AAAATTCAATTT
1 TAAATTTAATTT
450 CCAATAAGTC
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
16 15 0.42
17 15 0.42
18 6 0.17
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:6638 original size:22 final size:22
Alignment explanation
Indices: 6610--6654 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
6600 GAGCGAGCTC
6610 GATCTACGAGCTCAACTTGCGA
1 GATCTACGAGCTCAACTTGCGA
* *
6632 GATCTACGATCTCATCTTGCGA
1 GATCTACGAGCTCAACTTGCGA
6654 G
1 G
6655 TTCATTAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (22 bp):
GATCTACGAGCTCAACTTGCGA
Found at i:18947 original size:22 final size:22
Alignment explanation
Indices: 18922--18966 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
18912 CTCAAAATCT
* *
18922 ATAAATTTATAAGTTAATAATA
1 ATAAAATTACAAGTTAATAATA
*
18944 ATAAAATTACAATTTAATAATA
1 ATAAAATTACAAGTTAATAATA
18966 A
1 A
18967 AATAATAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
ATAAAATTACAAGTTAATAATA
Found at i:20574 original size:20 final size:21
Alignment explanation
Indices: 20532--20572 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
20522 ATATATTTTT
20532 ATAATTTTAATGATTTTAAAA
1 ATAATTTTAATGATTTTAAAA
20553 ATAATTTT-AT-ATTTTAAAA
1 ATAATTTTAATGATTTTAAAA
20572 A
1 A
20573 ATTAAATGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 2 0.10
21 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATAATTTTAATGATTTTAAAA
Found at i:21620 original size:14 final size:14
Alignment explanation
Indices: 21597--21648 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
21587 CATCTCCTCT
* *
21597 CTTTTTTTTTTTTA
1 CTTTTCTTTTTCTA
* *
21611 ATTTTCTTTTTGT-
1 CTTTTCTTTTTCTA
*
21624 CTCTTCTTTTTCTA
1 CTTTTCTTTTTCTA
21638 CTTTTCTTTTT
1 CTTTTCTTTTT
21649 ATTTTGATTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
13 10 0.33
14 20 0.67
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.77
Consensus pattern (14 bp):
CTTTTCTTTTTCTA
Found at i:25094 original size:6 final size:6
Alignment explanation
Indices: 25049--25091 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
25039 AAATCAGACC
* *
25049 TTTG-T TTTGTC TCTGTT TTTGTT TTTGTT TTTGTT TTT-TT TTT
1 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTT
25092 TTTAAAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 9 0.27
6 24 0.73
ACGTcount: A:0.00, C:0.05, G:0.14, T:0.81
Consensus pattern (6 bp):
TTTGTT
Found at i:33493 original size:117 final size:117
Alignment explanation
Indices: 33156--33787 Score: 574
Period size: 117 Copynumber: 5.3 Consensus size: 117
33146 CAGTTCCCGA
** * * * *
33156 CAATCACATAAAAACCAACTGCAAAAACTCACTCGTAAACCGAGCTCACCGAC-TGTTCAAAAGA
1 CAATCACATACCAACCAACTGCAATAATTCACTCGAAAACCGAACTCACCGACGT-TTC--AAGA
* ** * * *
33220 CTAAAATCTTCACTCCCATACATAAATCTCAAATACCATAAACTCGGTTTTCCAG
63 CTAAAATCTTCACTCCTATATGTATATCTCAAACACCCTAAACTCGGTTTTCCAG
* * * * * *
33275 CAATCACATACCAACCAACTGCAAAAAACTCACTCGTAAACCAAACTCGCCGACATTTCAAGACT
1 CAATCACATACCAACCAACTGC-AATAATTCACTCGAAAACCGAACTCACCGACGTTTCAAGACT
* * * * *
33340 AAAATCTTCACACCTATACGT-TAATCTCAAACGCCCTAACCTCAGTTTTCCAG
65 AAAATCTTCACTCCTATATGTAT-ATCTCAAACACCCTAAACTCGGTTTTCCAG
* * * * * **
33393 CAATCACGTGCCAACCAACTGCAATAATTCACTCGAAAACTGAACTCACTGATGTTTTGAGACTA
1 CAATCACATACCAACCAACTGCAATAATTCACTCGAAAACCGAACTCACCGACGTTTCAAGACTA
* * ** *
33458 CAATCCTCACTCCTATATGTATATCTCAAATGCCCTAAACTCAGTTTTCCAG
66 AAATCTTCACTCCTATATGTATATCTCAAACACCCTAAACTCGGTTTTCCAG
* * ** * * *
33510 CAACCACATACCAACCAAATGCAATAAACCACTTGTAAACCGAACTCACCAACAG-TTCAAGACT
1 CAATCACATACCAACCAACTGCAATAATTCACTCGAAAACCGAACTCACCGAC-GTTTCAAGACT
* * *
33574 AAAATCTTCACTCCTATATGTATATTTCAAACACCATAAACTCGGTTTTCCGG
65 AAAATCTTCACTCCTATATGTATATCTCAAACACCCTAAACTCGGTTTTCCAG
* **
33627 CAATCACATACCAAGTTACCAACCAAATGCAATACTTCACTCGAAAATTGAACTCA--GACGTTT
1 CAATCACATACC-A---ACCAA-C---TGCAATAATTCACTCGAAAACCGAACTCACCGACGTTT
* * * * **
33690 CTAGACAAAAATCCTCACTCCTATACT-TAAATCTCAAACACCCTAAACTCGGTTTTCTGG
58 CAAGACTAAAATCTTCACTCCTATA-TGTATATCTCAAACACCCTAAACTCGGTTTTCCAG
* * *
33750 CAATCACAAACCAATCAACTGCAATAATTCACTTGAAA
1 CAATCACATACCAACCAACTGCAATAATTCACTCGAAA
33788 CATCGAATCA
Statistics
Matches: 422, Mismatches: 76, Indels: 34
0.79 0.14 0.06
Matches are distributed among these distances:
115 17 0.04
117 180 0.43
118 73 0.17
119 24 0.06
120 31 0.07
121 6 0.01
122 2 0.00
123 66 0.16
124 1 0.00
125 22 0.05
ACGTcount: A:0.38, C:0.29, G:0.09, T:0.24
Consensus pattern (117 bp):
CAATCACATACCAACCAACTGCAATAATTCACTCGAAAACCGAACTCACCGACGTTTCAAGACTA
AAATCTTCACTCCTATATGTATATCTCAAACACCCTAAACTCGGTTTTCCAG
Found at i:34220 original size:16 final size:17
Alignment explanation
Indices: 34199--34234 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
34189 ACCAAAAGCC
34199 AAAATTAAAACTA-AGA
1 AAAATTAAAACTATAGA
*
34215 AAAATTGAAACTATAGA
1 AAAATTAAAACTATAGA
34232 AAA
1 AAA
34235 TGAAAGAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (17 bp):
AAAATTAAAACTATAGA
Found at i:35578 original size:62 final size:62
Alignment explanation
Indices: 35481--35618 Score: 242
Period size: 62 Copynumber: 2.2 Consensus size: 62
35471 TGCATTTACG
35481 ACAATGAAAAATAATTTTACTTAAAAATTAAAAGACACAATGATTATGGTTATACAATAAAT
1 ACAATGAAAAATAATTTTACTTAAAAATTAAAAGACACAATGATTATGGTTATACAATAAAT
***
35543 ACAATGAAAAATAATTTTACTTAAAAATTAAAAGACATGTTGATTATGGTTATACAATAAAT
1 ACAATGAAAAATAATTTTACTTAAAAATTAAAAGACACAATGATTATGGTTATACAATAAAT
35605 ACAATG-AAAATAAT
1 ACAATGAAAAATAAT
35619 ATTGGGCTTT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
61 8 0.11
62 65 0.89
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (62 bp):
ACAATGAAAAATAATTTTACTTAAAAATTAAAAGACACAATGATTATGGTTATACAATAAAT
Found at i:37090 original size:10 final size:10
Alignment explanation
Indices: 37061--37098 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
37051 GTTGATTTTA
37061 ATTAAAATTT
1 ATTAAAATTT
**
37071 -TTAATCTTT
1 ATTAAAATTT
37080 ATTAAAATTT
1 ATTAAAATTT
37090 ATTAAAATT
1 ATTAAAATT
37099 GTTTCAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTAAAATTT
Found at i:38315 original size:28 final size:28
Alignment explanation
Indices: 38284--38338 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
38274 TTTAAATTTA
**
38284 TTTAAATTTAAAATTTCCAAAATACATT
1 TTTAAATTTAAAAGGTCCAAAATACATT
*
38312 TTTAAATTTAAAAGGTCCAAATTACAT
1 TTTAAATTTAAAAGGTCCAAAATACAT
38339 GTTCCTAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (28 bp):
TTTAAATTTAAAAGGTCCAAAATACATT
Found at i:39875 original size:30 final size:30
Alignment explanation
Indices: 39777--39937 Score: 152
Period size: 30 Copynumber: 5.4 Consensus size: 30
39767 GTCTCTGAAC
* *
39777 TTTCTAGAAATCATATTTTAACCCTCAAACT
1 TTTCTA-AAATTACATTTTAACCCTCAAACT
* * *
39808 TCTCT-AAATTTCATTTTGACCC-CAAACT
1 TTTCTAAAATTACATTTTAACCCTCAAACT
* * * *
39836 TCTCCAAAATCACATTTTGACTCCT-AAACT
1 TTTCTAAAATTACATTTTAAC-CCTCAAACT
*
39866 TTTCTAAAATTACATGTTAACCCTCAAAC-
1 TTTCTAAAATTACATTTTAACCCTCAAACT
*
39895 TTCCTTAAAATTACA-TTTATACCCTCAAACT
1 TTTC-TAAAATTACATTTTA-ACCCTCAAACT
39926 TTTCTAAAATTA
1 TTTCTAAAATTA
39938 TGTTTTGATC
Statistics
Matches: 107, Mismatches: 16, Indels: 15
0.78 0.12 0.11
Matches are distributed among these distances:
28 10 0.09
29 35 0.33
30 55 0.51
31 7 0.07
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (30 bp):
TTTCTAAAATTACATTTTAACCCTCAAACT
Found at i:45191 original size:18 final size:18
Alignment explanation
Indices: 45168--45205 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
45158 TATTGATATC
45168 TTTATTATGT-TTTATTTT
1 TTTATT-TGTATTTATTTT
*
45186 TTTATTTTTATTTATTTT
1 TTTATTTGTATTTATTTT
45204 TT
1 TT
45206 GATATTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTATTTGTATTTATTTT
Found at i:45196 original size:14 final size:16
Alignment explanation
Indices: 45172--45203 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
45162 GATATCTTTA
45172 TTATGTTTTATTT-TT
1 TTATGTTTTATTTATT
45187 TTAT-TTTTATTTATT
1 TTATGTTTTATTTATT
45202 TT
1 TT
45204 TTGATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (16 bp):
TTATGTTTTATTTATT
Found at i:47964 original size:8 final size:9
Alignment explanation
Indices: 47926--48000 Score: 59
Period size: 9 Copynumber: 8.4 Consensus size: 9
47916 AAAGTATAAC
47926 AAATATATA
1 AAATATATA
*
47935 AAATAATCTA
1 AAAT-ATATA
*
47945 CAATAT-TA
1 AAATATATA
47953 AAATATAT-
1 AAATATATA
47961 AAATATATTA
1 AAATATA-TA
47971 AAAT-TATCA
1 AAATATAT-A
*
47980 AAATA-AAA
1 AAATATATA
*
47988 AAATCTATA
1 AAATATATA
47997 AAAT
1 AAAT
48001 TCAAATAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
8 20 0.38
9 22 0.42
10 11 0.21
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (9 bp):
AAATATATA
Found at i:47982 original size:27 final size:27
Alignment explanation
Indices: 47926--48001 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 27
47916 AAAGTATAAC
* *
47926 AAATATATAAA-ATAATCTACAA-TATTA
1 AAATATATAAATAT-AT-TAAAATTATCA
47953 AAATATATAAATATATTAAAATTATCA
1 AAATATATAAATATATTAAAATTATCA
* * *
47980 AAATAAAAAAATCTA-TAAAATT
1 AAATATATAAATATATTAAAATT
48002 CAAATAAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
26 11 0.26
27 29 0.69
28 2 0.05
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (27 bp):
AAATATATAAATATATTAAAATTATCA
Found at i:47991 original size:35 final size:35
Alignment explanation
Indices: 47926--47998 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
47916 AAAGTATAAC
* **
47926 AAATATATAAAATAATCTACAATATTAAAATATAT
1 AAATATATAAAATAATCTAAAATAAAAAAATATAT
* *
47961 AAATATATTAAAATTATC-AAAATAAAAAAATCTAT
1 AAATATA-TAAAATAATCTAAAATAAAAAAATATAT
47996 AAA
1 AAA
47999 ATTCAAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 23 0.72
36 9 0.28
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (35 bp):
AAATATATAAAATAATCTAAAATAAAAAAATATAT
Done.