Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014618.1 Kokia drynarioides strain JFW-HI SEQ_129657, 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: 46244
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:1814 original size:19 final size:22
Alignment explanation
Indices: 1792--1837 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1782 GTCTTATGAT
1792 TTTTAT-A-CTTTTT-ATAATA
1 TTTTATAAGCTTTTTAATAATA
* *
1811 TTTTGTAAGCTTTTTAATAATT
1 TTTTATAAGCTTTTTAATAATA
1833 TTTTA
1 TTTTA
1838 CATCTTCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.24
20 1 0.05
21 6 0.29
22 9 0.43
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.63
Consensus pattern (22 bp):
TTTTATAAGCTTTTTAATAATA
Found at i:10904 original size:221 final size:221
Alignment explanation
Indices: 10513--11177 Score: 1116
Period size: 221 Copynumber: 3.0 Consensus size: 221
10503 GTAGGTTGCT
* * * *
10513 TTGTTATGCTGTATACTATTGTATAATTCCTTGCTATGTTATTCGGACTCGAGTGCAAGTATCAA
1 TTGTTATGCGGTATACTATCGTATAATTCCTTGCTATGTTGTTCTGACTCGAGTGCAAGTATCAA
* * *
10578 ACATGGGTATATGCCCGACTCGGCTATATTCAATTTGTTTCAAGTTTTTTCATGTATTTAGAAGC
66 ACATGGGTATATACCCGACTCGGCTATGTTCAATTTGTTTCAAGTTTTTTCATGTATTTAGAGGC
* * *
10643 TCTTTTGAAAATTATATCTCCACACCTAAGGTCAAATACGTGTCGGACACAGTACTTAAAGCCAA
131 TCTTTTGAAAATTATATCTCCACACCTATGGTCCAATACGTGTCGGACACGGTACTTAAAGCCAA
*
10708 ATGAAGAGTCGAAGCAATTTCTGATC
196 ATGAAGAGTCGAAGCAATTTCCGATC
* * * *
10734 TTGTTATGCGGTATACTATCGTATGATTCCTTGCTATGTTGTTCTGACTTGAGTGCGACTATCAA
1 TTGTTATGCGGTATACTATCGTATAATTCCTTGCTATGTTGTTCTGACTCGAGTGCAAGTATCAA
* *
10799 ACATGGGTATATACCCGACTCGGCTATGTTCAATTTGTTTCAAATTATTTCATGTATTTAGAGGC
66 ACATGGGTATATACCCGACTCGGCTATGTTCAATTTGTTTCAAGTTTTTTCATGTATTTAGAGGC
10864 TCTTTTGAAAATTATATCTCCACACCTATGGTCCAATACGTGTCGGACACGGTACTTAAAGCCAA
131 TCTTTTGAAAATTATATCTCCACACCTATGGTCCAATACGTGTCGGACACGGTACTTAAAGCCAA
*
10929 ATGTAGAGTCGAAGCAATTTCCGATC
196 ATGAAGAGTCGAAGCAATTTCCGATC
*
10955 TTGTTATGCGGAATACTATCGTATAATTCCTTGCTATGTTGTTCTGACTCGAGTGCAAGTATCAA
1 TTGTTATGCGGTATACTATCGTATAATTCCTTGCTATGTTGTTCTGACTCGAGTGCAAGTATCAA
*
11020 ACATGGGTATATAACCGACTCGGCTATGTTCAATTTGTTTCAAGTTTTTTCATGTATTTAGAGGC
66 ACATGGGTATATACCCGACTCGGCTATGTTCAATTTGTTTCAAGTTTTTTCATGTATTTAGAGGC
*
11085 TCTTTTGAAAATTATATCTCCACACCTATGG-CCAAATACGTGTAGGACACGGTACTTAAAGCCA
131 TCTTTTGAAAATTATATCTCCACACCTATGGTCC-AATACGTGTCGGACACGGTACTTAAAGCCA
*
11149 AATGAAGAGTCCAAGCAATTTCCGATC
195 AATGAAGAGTCGAAGCAATTTCCGATC
11176 TT
1 TT
11178 AAATAGTCAT
Statistics
Matches: 414, Mismatches: 29, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
220 2 0.00
221 412 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (221 bp):
TTGTTATGCGGTATACTATCGTATAATTCCTTGCTATGTTGTTCTGACTCGAGTGCAAGTATCAA
ACATGGGTATATACCCGACTCGGCTATGTTCAATTTGTTTCAAGTTTTTTCATGTATTTAGAGGC
TCTTTTGAAAATTATATCTCCACACCTATGGTCCAATACGTGTCGGACACGGTACTTAAAGCCAA
ATGAAGAGTCGAAGCAATTTCCGATC
Found at i:15713 original size:23 final size:22
Alignment explanation
Indices: 15671--15715 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
15661 CTATTTCAAA
*
15671 TATAAAATATTTATTTTTATAT
1 TATAAAATATTTATTATTATAT
15693 TATAAAA-ATTATAATTATTATAT
1 TATAAAATATT-T-ATTATTATAT
15716 ATTAAACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 8 0.40
23 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATAAAATATTTATTATTATAT
Found at i:19328 original size:23 final size:22
Alignment explanation
Indices: 19298--19373 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 22
19288 CGCTAGCGCA
19298 CTTACTGTTCAGCACTGT-GTGTG
1 CTTACTGTTC-GCACT-TCGTGTG
19321 CTTACTGTTTCGCACTTCGTGTG
1 CTTACTG-TTCGCACTTCGTGTG
* *
19344 CTTATTGTTTCGCACCTCGTGTG
1 CTTACTG-TTCGCACTTCGTGTG
*
19367 CCTACTG
1 CTTACTG
19374 ATTTGCGCTA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.02
23 43 0.91
24 3 0.06
ACGTcount: A:0.11, C:0.26, G:0.22, T:0.41
Consensus pattern (22 bp):
CTTACTGTTCGCACTTCGTGTG
Found at i:19409 original size:22 final size:22
Alignment explanation
Indices: 19366--19435 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
19356 CACCTCGTGT
** *
19366 GCCTACTGATTTGCGCTATGTGC
1 GCCTACTGA-TTGCATTGTGTGC
*
19389 GCCTACTGATTGCATTGTGTGT
1 GCCTACTGATTGCATTGTGTGC
19411 GCCTACTGGATTGCACTATGTGTGC
1 GCCTACT-GATTGCA-T-TGTGTGC
19436 TTACTGTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
22 16 0.41
23 16 0.41
24 1 0.03
25 6 0.15
ACGTcount: A:0.14, C:0.23, G:0.27, T:0.36
Consensus pattern (22 bp):
GCCTACTGATTGCATTGTGTGC
Found at i:19432 original size:23 final size:22
Alignment explanation
Indices: 19362--19441 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 22
19352 TTCGCACCTC
*
19362 GTGTGCCTACTGATTTGCGCTAT
1 GTGTGCCTACTGA-TTGCACTAT
* * *
19385 GTGCGCCTACTGATTGCATTGT
1 GTGTGCCTACTGATTGCACTAT
19407 GTGTGCCTACTGGATTGCACTAT
1 GTGTGCCTACT-GATTGCACTAT
*
19430 GTGTGCTTACTG
1 GTGTGCCTACTG
19442 TTTCCCCAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
22 17 0.35
23 31 0.65
ACGTcount: A:0.14, C:0.21, G:0.28, T:0.38
Consensus pattern (22 bp):
GTGTGCCTACTGATTGCACTAT
Found at i:20420 original size:17 final size:17
Alignment explanation
Indices: 20398--20431 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20388 AAAAAAATTC
*
20398 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
20415 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
20432 TTATTGTAAG
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:21232 original size:17 final size:17
Alignment explanation
Indices: 21193--21231 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
21183 TAATTTAATT
*
21193 TATTTGATATATTTAAA
1 TATTTTATATATTTAAA
21210 TATTTTATATA-TTAAA
1 TATTTTATATATTTAAA
21226 TATTTT
1 TATTTT
21232 TTAAAATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TATTTTATATATTTAAA
Found at i:23820 original size:26 final size:26
Alignment explanation
Indices: 23765--23841 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
23755 GCTAAACCTC
**
23765 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
23791 ATTAAATAAATTCAAATTTAAATAGA
1 ATTAAATAAATTCAAACATAAAAAGA
* *
23817 ATTAATTCCAAATTCAATCATAAAA
1 ATTAAAT--AAATTCAAACATAAAA
23842 TTAATTAATT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 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:0.32
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:26664 original size:25 final size:26
Alignment explanation
Indices: 26612--26664 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
26602 GCTAACCTTC
* *
26612 TGTTTCCTTTTCTTATTCAAAACTTT
1 TGTTTCCTTTCCTTATTCAAAACATT
*
26638 TGTTTCCTTTCCTTCTTCAAAA-ATT
1 TGTTTCCTTTCCTTATTCAAAACATT
26663 TG
1 TG
26665 CTGTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.55
Consensus pattern (26 bp):
TGTTTCCTTTCCTTATTCAAAACATT
Found at i:27862 original size:16 final size:17
Alignment explanation
Indices: 27814--27867 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 17
27804 GATCTCTTAA
*
27814 AATAAAATTTTATTATT
1 AATAAAATTTTATAATT
*
27831 --TAAGTATTTTATAATT
1 AATAA-AATTTTATAATT
*
27847 TATAAAATTTTA-AATT
1 AATAAAATTTTATAATT
27863 AATAA
1 AATAA
27868 TGATAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 3 0.10
16 18 0.60
17 6 0.20
18 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
AATAAAATTTTATAATT
Found at i:41529 original size:93 final size:91
Alignment explanation
Indices: 41407--41591 Score: 325
Period size: 93 Copynumber: 2.0 Consensus size: 91
41397 ATCCACCGTA
* *
41407 TACTGCCAACACTGCAGTGGGGTTTTAGGCTTCCTCGAACTTTCCTTTGTATTAATATATATGTT
1 TACTGCCAACACTGCAGTGGGCTTTTAGGCTTCCTCGAACTTTCCTTCGTATTAATATATATG-T
41472 TTTTAACTTTTTCAATTTATATAGATAT
65 TTTTAAC-TTTTCAATTTATATAGATAT
41500 TACTGCCAACACTGCAGTGGGCTTTTAGGCTTCCTCGAACTTTCCTTCGTATTAATATATATGTT
1 TACTGCCAACACTGCAGTGGGCTTTTAGGCTTCCTCGAACTTTCCTTCGTATTAATATATATGTT
*
41565 TTTAACTTTTCAATTTATGTAGATAT
66 TTTAACTTTTCAATTTATATAGATAT
41591 T
1 T
41592 GTGAAAGAAG
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
91 20 0.22
92 8 0.09
93 61 0.69
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.44
Consensus pattern (91 bp):
TACTGCCAACACTGCAGTGGGCTTTTAGGCTTCCTCGAACTTTCCTTCGTATTAATATATATGTT
TTTAACTTTTCAATTTATATAGATAT
Found at i:42720 original size:23 final size:24
Alignment explanation
Indices: 42689--42742 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
42679 GGGAGTCGGA
*
42689 GCCCTTATCAACCCCC-TAATTAC
1 GCCCCTATCAACCCCCTTAATTAC
42712 GCCCCTATCAACCCCCTTAATTAC
1 GCCCCTATCAACCCCCTTAATTAC
42736 GCCCCTA
1 GCCCCTA
42743 ATGTCAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.24, C:0.46, G:0.06, T:0.24
Consensus pattern (24 bp):
GCCCCTATCAACCCCCTTAATTAC
Done.