Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004589.1 Kokia drynarioides strain JFW-HI SEQ_118079, 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: 5201
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:149 original size:25 final size:25
Alignment explanation
Indices: 121--170 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
111 ACATGCCTAT
121 GTGATTTTATGTGATAAGTGATATA
1 GTGATTTTATGTGATAAGTGATATA
146 GTGATTTTATGTGATAAGTGATATA
1 GTGATTTTATGTGATAAGTGATATA
171 ATGAGCATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (25 bp):
GTGATTTTATGTGATAAGTGATATA
Found at i:228 original size:20 final size:19
Alignment explanation
Indices: 191--229 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
181 CTCACATGTC
*
191 AAAGTGAAAAATTGTTTTT
1 AAAGTGAAAAAGTGTTTTT
210 AAAGTGAAAAAGTGATTTTT
1 AAAGTGAAAAAGTG-TTTTT
230 GTGACCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38
Consensus pattern (19 bp):
AAAGTGAAAAAGTGTTTTT
Found at i:342 original size:46 final size:44
Alignment explanation
Indices: 274--374 Score: 148
Period size: 46 Copynumber: 2.2 Consensus size: 44
264 AAAGGTGGAA
* * *
274 GATGTGACAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATATT
1 GATGTGATAGTATATCTACAAAAGTGGTGGCTTGTCCACAAT-TT
*
319 GAATGTGGTAGTATATCTACAAAAGTGGTGGCTTGTCCACAATTT
1 G-ATGTGATAGTATATCTACAAAAGTGGTGGCTTGTCCACAATTT
364 GATGTGATAGT
1 GATGTGATAGT
375 TTGTCAGCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 9 0.18
45 4 0.08
46 37 0.74
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.34
Consensus pattern (44 bp):
GATGTGATAGTATATCTACAAAAGTGGTGGCTTGTCCACAATTT
Found at i:512 original size:19 final size:20
Alignment explanation
Indices: 471--513 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
461 GATGGGTAGG
* *
471 ATTGTTTTAATAAAATTTTC
1 ATTGTTTTAATAAAATGTGC
*
491 ATTGTTTT-ATGAAATGTGC
1 ATTGTTTTAATAAAATGTGC
510 ATTG
1 ATTG
514 ACTTGATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (20 bp):
ATTGTTTTAATAAAATGTGC
Found at i:1909 original size:15 final size:16
Alignment explanation
Indices: 1889--1918 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1879 CATGCCTGCA
1889 AAGACAAAA-AGAAAT
1 AAGACAAAAGAGAAAT
1904 AAGACAAAAGAGAAA
1 AAGACAAAAGAGAAA
1919 AACAATAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.07, G:0.17, T:0.03
Consensus pattern (16 bp):
AAGACAAAAGAGAAAT
Found at i:2487 original size:20 final size:20
Alignment explanation
Indices: 2462--2524 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
2452 AGGCGGTGAA
2462 CGACGGTCGATTGGGAATAG
1 CGACGGTCGATTGGGAATAG
2482 CGACGGTCGATTGGGAATAG
1 CGACGGTCGATTGGGAATAG
* *
2502 CGACGGTCGATGGGGAACAG
1 CGACGGTCGATTGGGAATAG
2522 CGA
1 CGA
2525 TGGTGGCGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.25, C:0.17, G:0.41, T:0.16
Consensus pattern (20 bp):
CGACGGTCGATTGGGAATAG
Found at i:2991 original size:30 final size:30
Alignment explanation
Indices: 2946--3082 Score: 161
Period size: 29 Copynumber: 4.6 Consensus size: 30
2936 AAATTTTTTA
* * *
2946 AAAATAACATTTTGACCCTCGAACTTTTCC
1 AAAATTACATATTGACCCTCAAACTTTTCC
*
2976 AAAATTACATATTGACCCTCAAA-TTTTTC
1 AAAATTACATATTGACCCTCAAACTTTTCC
* * *
3005 AAAATTACACATTGACCCTTAAAC-TTTCT
1 AAAATTACATATTGACCCTCAAACTTTTCC
* *
3034 AAAATTACATATTAACCCTCAAATTTTTCC
1 AAAATTACATATTGACCCTCAAACTTTTCC
* *
3064 AAAATTACATTTTAACCCT
1 AAAATTACATATTGACCCT
3083 AAATGCTCCG
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
29 49 0.54
30 42 0.46
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAATTACATATTGACCCTCAAACTTTTCC
Found at i:3012 original size:29 final size:29
Alignment explanation
Indices: 2932--3086 Score: 154
Period size: 29 Copynumber: 5.3 Consensus size: 29
2922 GCTAAGAGAT
* * *
2932 CCCT-AAATTTTTTAAAAATAACATTTTGA
1 CCCTCAAA-TTTTTCAAAATTACATATTGA
* *
2961 CCCTCGAACTTTTCCAAAATTACATATTGA
1 CCCTC-AAATTTTTCAAAATTACATATTGA
*
2991 CCCTCAAATTTTTCAAAATTACACATTGA
1 CCCTCAAATTTTTCAAAATTACATATTGA
* * *
3020 CCCTTAAA-CTTTCTAAAATTACATATTAA
1 CCCTCAAATTTTTC-AAAATTACATATTGA
* *
3049 CCCTCAAATTTTTCCAAAATTACATTTTAA
1 CCCTCAAATTTTT-CAAAATTACATATTGA
3079 CCCT-AAAT
1 CCCTCAAAT
3087 GCTCCGAGAC
Statistics
Matches: 106, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
28 4 0.04
29 56 0.53
30 43 0.41
31 3 0.03
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.37
Consensus pattern (29 bp):
CCCTCAAATTTTTCAAAATTACATATTGA
Found at i:3030 original size:59 final size:59
Alignment explanation
Indices: 2932--3072 Score: 180
Period size: 58 Copynumber: 2.4 Consensus size: 59
2922 GCTAAGAGAT
* * * *
2932 CCCT-AAATTTTTTAAAAATA-ACATTTTGACCCTCGAACTTTTCCAAAATTACATATTGA
1 CCCTCAAATTTTTCAAAATTACACA-TTTGACCCTCAAAC-TTTCCAAAATTACATATTAA
* *
2991 CCCTCAAATTTTTCAAAATTACACA-TTGACCCTTAAACTTTCTAAAATTACATATTAA
1 CCCTCAAATTTTTCAAAATTACACATTTGACCCTCAAACTTTCCAAAATTACATATTAA
3049 CCCTCAAATTTTTCCAAAATTACA
1 CCCTCAAATTTTT-CAAAATTACA
3073 TTTTAACCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
58 31 0.42
59 25 0.34
60 14 0.19
61 3 0.04
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (59 bp):
CCCTCAAATTTTTCAAAATTACACATTTGACCCTCAAACTTTCCAAAATTACATATTAA
Found at i:3082 original size:59 final size:59
Alignment explanation
Indices: 2932--3082 Score: 189
Period size: 59 Copynumber: 2.6 Consensus size: 59
2922 GCTAAGAGAT
* * * *
2932 CCCT-AAATTTTTTAAAAATAACATTTTGACCCTCGAACTTTTCCAAAATTACATATTGA
1 CCCTCAAA-TTTTTCAAAATTACATTTTGACCCTCAAACTTTTCCAAAATTACATATTAA
** * *
2991 CCCTCAAATTTTTCAAAATTACACATTGACCCTTAAAC-TTTCTAAAATTACATATTAA
1 CCCTCAAATTTTTCAAAATTACATTTTGACCCTCAAACTTTTCCAAAATTACATATTAA
*
3049 CCCTCAAATTTTTCCAAAATTACATTTTAACCCT
1 CCCTCAAATTTTT-CAAAATTACATTTTGACCCT
3083 AAATGCTCCG
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
58 31 0.39
59 45 0.57
60 3 0.04
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (59 bp):
CCCTCAAATTTTTCAAAATTACATTTTGACCCTCAAACTTTTCCAAAATTACATATTAA
Found at i:3225 original size:13 final size:15
Alignment explanation
Indices: 3194--3226 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
3184 TTAATCCTTT
3194 TTTTTGTATTCGATG
1 TTTTTGTATTCGATG
3209 TTTTTG-ATTCG-TG
1 TTTTTGTATTCGATG
3222 TTTTT
1 TTTTT
3227 CGTAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 5 0.28
15 6 0.33
ACGTcount: A:0.09, C:0.06, G:0.18, T:0.67
Consensus pattern (15 bp):
TTTTTGTATTCGATG
Done.