Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000933.1 Kokia drynarioides strain JFW-HI SEQ_112089, 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: 5066
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:1404 original size:29 final size:29
Alignment explanation
Indices: 1363--1588 Score: 178
Period size: 29 Copynumber: 7.9 Consensus size: 29
1353 ATTTTCTTTG
*
1363 AAAATTACATTTTTACCCTCGAACTTCTA
1 AAAATTACATTTTTACCCTCAAACTTCTA
* *
1392 AAAATTACA-TTTTACCCCCAAACTTCCA
1 AAAATTACATTTTTACCCTCAAACTTCTA
* * *
1420 AAAATCATATTTTTACCCTCAAATTTCTCA
1 AAAATTACATTTTTACCCTCAAACTTCT-A
** *
1450 AAAATTACATTTTGCCCCT-AAACTTCCA
1 AAAATTACATTTTTACCCTCAAACTTCTA
* *
1478 AAAA-T-CATATTTTCCCCCCAAACTTCTCA
1 AAAATTACAT-TTTTACCCTCAAACTTCT-A
* * *
1507 AAAATTACATTTTTGCTCGT-AAACTTTTA
1 AAAATTACATTTTTAC-CCTCAAACTTCTA
* * **
1536 AAAATTACTTTTTTGCCC-C-AACTTCCC
1 AAAATTACATTTTTACCCTCAAACTTCTA
* * *
1563 AAAATTACGTTTTTGCCCTTAAACTT
1 AAAATTACATTTTTACCCTCAAACTT
1589 TCCAAAATTA
Statistics
Matches: 158, Mismatches: 28, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
26 3 0.02
27 30 0.19
28 36 0.23
29 56 0.35
30 29 0.18
31 4 0.03
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAATTACATTTTTACCCTCAAACTTCTA
Found at i:1473 original size:58 final size:58
Alignment explanation
Indices: 1371--1519 Score: 230
Period size: 57 Copynumber: 2.6 Consensus size: 58
1361 TGAAAATTAC
*
1371 ATTTTTACCCTCGAACTTCT-AAAAATTACATTTTACCCCCAAACTTCCAAAAATCAT
1 ATTTTTACCCTCAAACTTCTCAAAAATTACATTTTACCCCCAAACTTCCAAAAATCAT
* * *
1428 ATTTTTACCCTCAAATTTCTCAAAAATTACATTTTGCCCCTAAACTTCCAAAAATCAT
1 ATTTTTACCCTCAAACTTCTCAAAAATTACATTTTACCCCCAAACTTCCAAAAATCAT
* *
1486 A-TTTTCCCCCCAAACTTCTCAAAAATTACATTTT
1 ATTTTTACCCTCAAACTTCTCAAAAATTACATTTT
1520 TGCTCGTAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
57 48 0.57
58 36 0.43
ACGTcount: A:0.36, C:0.28, G:0.01, T:0.36
Consensus pattern (58 bp):
ATTTTTACCCTCAAACTTCTCAAAAATTACATTTTACCCCCAAACTTCCAAAAATCAT
Found at i:1521 original size:58 final size:57
Alignment explanation
Indices: 1373--1595 Score: 220
Period size: 58 Copynumber: 3.9 Consensus size: 57
1363 AAAATTACAT
* * * *
1373 TTTTACCCTCGAACTTCT-AAAAATTACATTTTACCCCCAAACTTCCAAAAATCATA
1 TTTTACCCCCAAACTTCTCAAAAATTACATTTTGCCCCTAAACTTCCAAAAATCATA
* *
1429 TTTTTACCCTCAAATTTCTCAAAAATTACATTTTGCCCCTAAACTTCCAAAAATCATA
1 -TTTTACCCCCAAACTTCTCAAAAATTACATTTTGCCCCTAAACTTCCAAAAATCATA
* * * ** *
1487 TTTTCCCCCCAAACTTCTCAAAAATTACATTTTTGCTCGTAAACTTTTAAAAATTACT-
1 TTTTACCCCCAAACTTCTCAAAAATTACA-TTTTGCCCCTAAACTTCCAAAAATCA-TA
** * * *
1545 TTTTTGCCCC-AACTTC-CCAAAATTACGTTTTTGCCCTTAAACTTTCCAAAA
1 TTTTACCCCCAAACTTCTCAAAAATTAC-ATTTTGCCCCTAAAC-TTCCAAAA
1596 TTATGTTTTA
Statistics
Matches: 141, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
56 21 0.15
57 54 0.38
58 65 0.46
59 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (57 bp):
TTTTACCCCCAAACTTCTCAAAAATTACATTTTGCCCCTAAACTTCCAAAAATCATA
Found at i:1755 original size:14 final size:14
Alignment explanation
Indices: 1736--1769 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1726 CGATTTGTAT
*
1736 TTTATTTTCTTATA
1 TTTATTTTCATATA
1750 TTTATTTTCATATA
1 TTTATTTTCATATA
1764 TTTATT
1 TTTATT
1770 CATTCGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATTTTCATATA
Found at i:2999 original size:2 final size:2
Alignment explanation
Indices: 2992--3036 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
2982 TGAAATTTGT
*
2992 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC GC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3034 TC T
1 TC T
3037 TTGCGTTTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
TC
Found at i:4304 original size:53 final size:53
Alignment explanation
Indices: 4224--4330 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
4214 ATAATAGGAG
4224 GGGCCATGGTTCGGTCAGGGAAAGATTGGACCTTTTTTTGTCTCCACAAGCTA
1 GGGCCATGGTTCGGTCAGGGAAAGATTGGACCTTTTTTTGTCTCCACAAGCTA
*
4277 GGGCCATGGTTTGGTCAGGGAAAGATTGGACCTTTTTTTGTCTCCACAAGCTA
1 GGGCCATGGTTCGGTCAGGGAAAGATTGGACCTTTTTTTGTCTCCACAAGCTA
4330 G
1 G
4331 CTTAGGAGCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.31
Consensus pattern (53 bp):
GGGCCATGGTTCGGTCAGGGAAAGATTGGACCTTTTTTTGTCTCCACAAGCTA
Done.