Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003943.1 Kokia drynarioides strain JFW-HI SEQ_117027, 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: 8872
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Found at i:42 original size:32 final size:32
Alignment explanation
Indices: 1--64 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1 ATATATATATATATATAACCAATACGTGTCAT
1 ATATATATATATATATAACCAATACGTGTCAT
33 ATATATATATATATATAACCAATACGTGTCAT
1 ATATATATATATATATAACCAATACGTGTCAT
65 TGCTTTGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (32 bp):
ATATATATATATATATAACCAATACGTGTCAT
Found at i:2977 original size:17 final size:18
Alignment explanation
Indices: 2957--2990 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2947 TTGTTAAGTT
2957 TTGTATT-TCTTTATTTA
1 TTGTATTATCTTTATTTA
*
2974 TTGTATTATTTTTATTT
1 TTGTATTATCTTTATTT
2991 GATTTAGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.74
Consensus pattern (18 bp):
TTGTATTATCTTTATTTA
Found at i:3341 original size:9 final size:9
Alignment explanation
Indices: 3329--3366 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
3319 TTAAATTTTT
3329 TAATTCGAA
1 TAATTCGAA
3338 TAATTCGAA
1 TAATTCGAA
*
3347 TAATTCAAA
1 TAATTCGAA
*
3356 TAAATCGAA
1 TAATTCGAA
3365 TA
1 TA
3367 TCAAACTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (9 bp):
TAATTCGAA
Found at i:3399 original size:28 final size:28
Alignment explanation
Indices: 3368--3426 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
3358 AATCGAATAT
* *
3368 CAAACTATAATATTTTATATTTTTACCC
1 CAAACCATAAAATTTTATATTTTTACCC
* * *
3396 CAAACCCTAAAATTTTTTATTTTTCCCC
1 CAAACCATAAAATTTTATATTTTTACCC
3424 CAA
1 CAA
3427 TACTTTTACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.42
Consensus pattern (28 bp):
CAAACCATAAAATTTTATATTTTTACCC
Found at i:6809 original size:27 final size:27
Alignment explanation
Indices: 6563--6820 Score: 183
Period size: 27 Copynumber: 9.6 Consensus size: 27
6553 AAGGAAAGAA
* * *
6563 AAGCCTTCGTGGCAAATCATTAATGAG
1 AAGCCTTTGTGGCAAATCATGAATGAT
* *
6590 AAGCCATTGTGACAAATCATGAATGA-
1 AAGCCTTTGTGGCAAATCATGAATGAT
6616 ATAGCC-TTGTGGCAAATCATGAATGAAT
1 A-AGCCTTTGTGGCAAATCATGAATG-AT
* *
6644 AA-CCTTTATGGCAAATCATGAATGGGT
1 AAGCCTTTGTGGCAAATCATGAAT-GAT
* *
6671 -ATCCTTTGTGGAAAATCATGAATGGAT
1 AAGCCTTTGTGGCAAATCATGAAT-GAT
** ** *
6698 -AGTTTTTGTTACAAGTCATGAATGAAT
1 AAGCCTTTGTGGCAAATCATGAATG-AT
* * *
6725 AA-CCATTATGGCAAGTCATGAATGACT
1 AAGCCTTTGTGGCAAATCATGAATGA-T
* *
6752 AA--CTTTCGTGGCAAGTCATGAAT-AA
1 AAGCCTTT-GTGGCAAATCATGAATGAT
* *
6777 ATAGCCTTTGTGGCGAATCATGAAAGAT
1 A-AGCCTTTGTGGCAAATCATGAATGAT
*
6805 AAGCCCTTGTGGCAAA
1 AAGCCTTTGTGGCAAA
6821 CTATGAAGGA
Statistics
Matches: 185, Mismatches: 32, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
25 1 0.01
26 29 0.16
27 146 0.79
28 9 0.05
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (27 bp):
AAGCCTTTGTGGCAAATCATGAATGAT
Found at i:6817 original size:54 final size:54
Alignment explanation
Indices: 6564--6833 Score: 228
Period size: 54 Copynumber: 5.0 Consensus size: 54
6554 AGGAAAGAAA
* * * * *
6564 AGCCTTCGTGGCAAATCATTAATGAGAAGCCATTGTGACAAATCATGAATGAAT
1 AGCCTTTGTGGCAAATCATGAATGATAAGCCTTTGTGGCAAATCATGAATGAAT
* **
6618 AGCC-TTGTGGCAAATCATGAATGAATAA-CCTTTATGGCAAATCATGAATGGGT
1 AGCCTTTGTGGCAAATCATGAATG-ATAAGCCTTTGTGGCAAATCATGAATGAAT
* * ** ** *
6671 ATCCTTTGTGGAAAATCATGAATGGAT-AGTTTTTGTTACAAGTCATGAATGAAT
1 AGCCTTTGTGGCAAATCATGAAT-GATAAGCCTTTGTGGCAAATCATGAATGAAT
* * * * * *
6725 AACCATTATGGCAAGTCATGAATGACTAA--CTTTCGTGGCAAGTCATGAATAAAT
1 AGCCTTTGTGGCAAATCATGAATGA-TAAGCCTTT-GTGGCAAATCATGAATGAAT
* * * *
6779 AGCCTTTGTGGCGAATCATGAAAGATAAGCCCTTGTGGCAAA-CTATGAAGGAAT
1 AGCCTTTGTGGCAAATCATGAATGATAAGCCTTTGTGGCAAATC-ATGAATGAAT
6833 A
1 A
6834 TACCTCATGA
Statistics
Matches: 169, Mismatches: 37, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
53 50 0.30
54 114 0.67
55 5 0.03
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (54 bp):
AGCCTTTGTGGCAAATCATGAATGATAAGCCTTTGTGGCAAATCATGAATGAAT
Found at i:6819 original size:81 final size:80
Alignment explanation
Indices: 6603--6800 Score: 229
Period size: 81 Copynumber: 2.5 Consensus size: 80
6593 CCATTGTGAC
*
6603 AAATCATGAATGAATAGCC-TTGTGGCAAATCATGAATGAATAACCTTTATGGCAAATCATGAAT
1 AAATCATGAATGAATAGCCTTTGTGGC-AATCATGAATGAATAACCATTATGGCAAATCATGAAT
** *
6667 GGGTATCCTTTGTGGA
65 GACTATACTTTGTGGA
* ** ** *
6683 AAATCATGAATGGATAGTTTTTGTTACAAGTCATGAATGAATAACCATTATGGCAAGTCATGAAT
1 AAATCATGAATGAATAGCCTTTGTGGCAA-TCATGAATGAATAACCATTATGGCAAATCATGAAT
*
6748 GACTA-ACTTTCGTGGC
65 GACTATACTTT-GTGGA
* *
6764 AAGTCATGAATAAATAGCCTTTGTGGCGAATCATGAA
1 AAATCATGAATGAATAGCCTTTGTGGC-AATCATGAA
6801 AGATAAGCCC
Statistics
Matches: 96, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
80 22 0.23
81 72 0.75
82 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (80 bp):
AAATCATGAATGAATAGCCTTTGTGGCAATCATGAATGAATAACCATTATGGCAAATCATGAATG
ACTATACTTTGTGGA
Done.