Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014879.1 Kokia drynarioides strain JFW-HI SEQ_129922, 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: 283654
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 221 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:250745 original size:13 final size:13
Alignment explanation
Indices: 250727--250754 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
250717 GCTTGCCCAT
250727 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
250740 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
250753 AA
1 AA
250755 GGGGAAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:271882 original size:18 final size:18
Alignment explanation
Indices: 271861--271902 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
271851 TTAATTTTGT
*
271861 TAATTC-GGTTAATTCGAG
1 TAATTCAGG-TAATTCCAG
271879 TAATTCAGGTAATTCCAG
1 TAATTCAGGTAATTCCAG
271897 TAATTC
1 TAATTC
271903 CATTAATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (18 bp):
TAATTCAGGTAATTCCAG
Found at i:271891 original size:27 final size:27
Alignment explanation
Indices: 271842--271893 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
271832 ATTCAATACT
* ** *
271842 TTAATTCGATTAATTTTGTTAATTCGG
1 TTAATTCGAGTAATTCAGGTAATTCGG
271869 TTAATTCGAGTAATTCAGGTAATTC
1 TTAATTCGAGTAATTCAGGTAATTC
271894 CAGTAATTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (27 bp):
TTAATTCGAGTAATTCAGGTAATTCGG
Found at i:272017 original size:30 final size:30
Alignment explanation
Indices: 271981--272062 Score: 146
Period size: 30 Copynumber: 2.7 Consensus size: 30
271971 CCGAATTAAC
271981 TGAAAAATTTCGGTTTGATTAATATTTTTT
1 TGAAAAATTTCGGTTTGATTAATATTTTTT
*
272011 TGAAAAATTTCGGTTTGATTAATTTTTTTT
1 TGAAAAATTTCGGTTTGATTAATATTTTTT
*
272041 TGAAAAATTTTGGTTTGATTAA
1 TGAAAAATTTCGGTTTGATTAA
272063 CGATTATAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.52
Consensus pattern (30 bp):
TGAAAAATTTCGGTTTGATTAATATTTTTT
Found at i:272027 original size:15 final size:15
Alignment explanation
Indices: 271981--272058 Score: 52
Period size: 15 Copynumber: 5.2 Consensus size: 15
271971 CCGAATTAAC
271981 TGAAAAATTTCGGTT
1 TGAAAAATTTCGGTT
* *
271996 TGATTAATATTT--TTT
1 TGA--AAAATTTCGGTT
272011 TGAAAAATTTCGGTT
1 TGAAAAATTTCGGTT
** ***
272026 TGATTAATTTTTTTT
1 TGAAAAATTTCGGTT
*
272041 TGAAAAATTTTGGTT
1 TGAAAAATTTCGGTT
272056 TGA
1 TGA
272059 TTAACGATTA
Statistics
Matches: 46, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
13 6 0.13
15 34 0.74
17 6 0.13
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (15 bp):
TGAAAAATTTCGGTT
Found at i:279033 original size:24 final size:24
Alignment explanation
Indices: 278979--279033 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
278969 ACTTCTCACA
278979 CTTTTTCTTACTCTTTTCTTTTTT
1 CTTTTTCTTACTCTTTTCTTTTTT
* *
279003 GTATTTC-TACTCATTTT-TTTTGTT
1 CTTTTTCTTACTC-TTTTCTTTT-TT
279027 CTTTTTC
1 CTTTTTC
279034 ACTTGTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (24 bp):
CTTTTTCTTACTCTTTTCTTTTTT
Found at i:280788 original size:47 final size:47
Alignment explanation
Indices: 280737--280830 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
280727 AATAGCTTGG
*
280737 TTAAAATTGGATTGTGTGTCAGTGTCGGGTCTAACATTCCACACACC
1 TTAAAATTAGATTGTGTGTCAGTGTCGGGTCTAACATTCCACACACC
280784 TTAAAATTAGATTGTGTGTCAGTGTCGGGTCTAACATTCCACACACC
1 TTAAAATTAGATTGTGTGTCAGTGTCGGGTCTAACATTCCACACACC
280831 CCTCCCCTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (47 bp):
TTAAAATTAGATTGTGTGTCAGTGTCGGGTCTAACATTCCACACACC
Found at i:282348 original size:25 final size:25
Alignment explanation
Indices: 282315--282371 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
282305 GATTGTTAAA
282315 AGAACTTCTAAAAAAAAAACTC-AAG
1 AGAA-TTCTAAAAAAAAAACTCAAAG
** *
282340 AGCAATTCTTGAATAAAAACTCAAAG
1 AG-AATTCTAAAAAAAAAACTCAAAG
282366 AGAATT
1 AGAATT
282372 ATTATTAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 20 0.74
26 7 0.26
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.21
Consensus pattern (25 bp):
AGAATTCTAAAAAAAAAACTCAAAG
Found at i:283436 original size:24 final size:24
Alignment explanation
Indices: 283404--283459 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
283394 TGTATGGGTA
283404 TCTTCTTGTTTTTCATTTTCTGTT
1 TCTTCTTGTTTTTCATTTTCTGTT
*
283428 TCTTCTTGTTTTTCATTTTCTTTT
1 TCTTCTTGTTTTTCATTTTCTGTT
*
283452 TCCTCTTG
1 TCTTCTTG
283460 AGAACTCTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.04, C:0.20, G:0.07, T:0.70
Consensus pattern (24 bp):
TCTTCTTGTTTTTCATTTTCTGTT
Done.