Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012121.1 Kokia drynarioides strain JFW-HI SEQ_127120, 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: 2310
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.34
Warning! 135 characters in sequence are not A, C, G, or T
Found at i:397 original size:24 final size:24
Alignment explanation
Indices: 368--413 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
358 TTATATATTA
368 AATAATTTCATTAATGAAAATAAT
1 AATAATTTCATTAATGAAAATAAT
* *
392 AATAATTTTATTAATGATAATA
1 AATAATTTCATTAATGAAAATA
414 TTTATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (24 bp):
AATAATTTCATTAATGAAAATAAT
Found at i:428 original size:24 final size:24
Alignment explanation
Indices: 386--456 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
376 CATTAATGAA
386 AATAATAATAATT--T-TATTAAT
1 AATAATAATAATTAATATATTAAT
* * *
407 GATAATATTTATTAA-ATAATTAAT
1 AATAATAATAATTAATAT-ATTAAT
431 AATAATAATAATTAATATATTAAT
1 AATAATAATAATTAATATATTAAT
455 AA
1 AA
457 AAAAGAAAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
21 10 0.26
23 1 0.03
24 26 0.67
25 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (24 bp):
AATAATAATAATTAATATATTAAT
Found at i:440 original size:16 final size:15
Alignment explanation
Indices: 421--456 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
411 ATATTTATTA
421 AATAATTAATAATAAT
1 AATAATTAAT-ATAAT
*
437 AATAATTAATATATT
1 AATAATTAATATAAT
452 AATAA
1 AATAA
457 AAAAGAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATAATTAATATAAT
Found at i:1558 original size:29 final size:30
Alignment explanation
Indices: 1526--1696 Score: 137
Period size: 29 Copynumber: 5.9 Consensus size: 30
1516 TTTGACCTTG
1526 AAACTTCT-AAAAATTACATTTTTACCCCC
1 AAACTTCTCAAAAATTACATTTTTACCCCC
* *
1555 AAACTT-TCACAAATTACATGTTTACCCCC
1 AAACTTCTCAAAAATTACATTTTTACCCCC
* * * **
1584 GAACTT-TCAAAAATTTCATTTTAACCCTA
1 AAACTTCTCAAAAATTACATTTTTACCCCC
*
1613 AAACTTCT-AAAAATTACCA-TTTTACCCCT
1 AAACTTCTCAAAAATTA-CATTTTTACCCCC
* * * *
1642 AAACTTC-C--AAACTCCATTTTTTACCTCG
1 AAACTTCTCAAAAATTACA-TTTTTACCCCC
1670 AAACTT-TCAAAAATTATCA-TTTTACCC
1 AAACTTCTCAAAAATTA-CATTTTTACCC
1697 TCGAATGTCC
Statistics
Matches: 111, Mismatches: 21, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
26 2 0.02
27 4 0.04
28 16 0.14
29 80 0.72
30 7 0.06
31 2 0.02
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (30 bp):
AAACTTCTCAAAAATTACATTTTTACCCCC
Found at i:1596 original size:58 final size:57
Alignment explanation
Indices: 1527--1701 Score: 158
Period size: 58 Copynumber: 3.0 Consensus size: 57
1517 TTGACCTTGA
* *
1527 AACTTCTAAAAATTACATTTTTACCCCCAAACTTTCACAAATTA-CATGTTTACCCCCG
1 AACTTC-AAAAATTACATTTTTACCCCAAAACTTTCAAAAATTACCAT-TTTACCCCCG
* * * **
1585 AACTTTCAAAAATTTCATTTTAACCCTAAAAC-TTCTAAAAATTACCATTTTACCCCTA
1 AAC-TTCAAAAATTACATTTTTACCCCAAAACTTTC-AAAAATTACCATTTTACCCCCG
* * * * * * *
1643 AACTTC-CAAACTCCATTTTTTACCTCGAAACTTTCAAAAATTATCATTTTACCCTCG
1 AACTTCAAAAATTACA-TTTTTACCCCAAAACTTTCAAAAATTACCATTTTACCCCCG
1700 AA
1 AA
1702 TGTCCAAAAA
Statistics
Matches: 94, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
56 6 0.06
57 37 0.39
58 45 0.48
59 6 0.06
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (57 bp):
AACTTCAAAAATTACATTTTTACCCCAAAACTTTCAAAAATTACCATTTTACCCCCG
Found at i:1690 original size:87 final size:87
Alignment explanation
Indices: 1504--1697 Score: 238
Period size: 87 Copynumber: 2.2 Consensus size: 87
1494 CTAAACTATC
* *
1504 CAAAAATTAT-ATTTTGACCTTGAAACTTCTAAAAATTACATTTTTACCCCCAAACTTTCACAAA
1 CAAAAATTATCATTTT-ACCCTAAAACTTCTAAAAATTACATTTTTACCCCCAAACTTTCACAAA
*
1568 TTACATGTTTACCCCCGAACTTT
65 CTACATGTTTACCCCCGAACTTT
*
1591 CAAAAATT-TCATTTTAACCCTAAAACTTCTAAAAATTACCA-TTTTACCCCTAAAC-TTC-CAA
1 CAAAAATTATCATTTT-ACCCTAAAACTTCTAAAAATTA-CATTTTTACCCCCAAACTTTCACAA
* * *
1652 ACTCCATTTTTTA-CCTCGAAACTTT
64 ACTACA-TGTTTACCCCCG-AACTTT
1677 CAAAAATTATCATTTTACCCT
1 CAAAAATTATCATTTTACCCT
1698 CGAATGTCCA
Statistics
Matches: 94, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
85 11 0.12
86 28 0.30
87 53 0.56
88 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (87 bp):
CAAAAATTATCATTTTACCCTAAAACTTCTAAAAATTACATTTTTACCCCCAAACTTTCACAAAC
TACATGTTTACCCCCGAACTTT
Found at i:1851 original size:27 final size:28
Alignment explanation
Indices: 1794--1854 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
1784 CCTAAATTTC
* *
1794 TCCAAAATTACCATTTTTCCCTCGAGAA
1 TCCAAAATTACCATTTTGCCCCCGAGAA
*
1822 TCCAAAATTACCATTTTGCCCCCGA-TA
1 TCCAAAATTACCATTTTGCCCCCGAGAA
1849 TCCAAA
1 TCCAAA
1855 CAATCTCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.33, C:0.31, G:0.07, T:0.30
Consensus pattern (28 bp):
TCCAAAATTACCATTTTGCCCCCGAGAA
Found at i:2179 original size:14 final size:14
Alignment explanation
Indices: 2160--2186 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2150 CGAAAGAATC
2160 GAATACCTTTAATT
1 GAATACCTTTAATT
2174 GAATACCTTTAAT
1 GAATACCTTTAAT
2187 CGAGGCAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (14 bp):
GAATACCTTTAATT
Done.