Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013060.1 Kokia drynarioides strain JFW-HI SEQ_128078, 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: 84446
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:3088 original size:15 final size:15
Alignment explanation
Indices: 3068--3114 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
3058 ATAAAACGAT
3068 AACATAAATAATTAA
1 AACATAAATAATTAA
* *
3083 AACAT-AATATTTCA
1 AACATAAATAATTAA
*
3097 AATATAAATAATTAA
1 AACATAAATAATTAA
3112 AAC
1 AAC
3115 GTACTCTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.30
Consensus pattern (15 bp):
AACATAAATAATTAA
Found at i:5938 original size:19 final size:19
Alignment explanation
Indices: 5914--5958 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
5904 TGAACATTTT
5914 GACTTATTGGAATAAGCTA
1 GACTTATTGGAATAAGCTA
5933 GACTTATTGGAATAAGCTA
1 GACTTATTGGAATAAGCTA
*
5952 GTCTTAT
1 GACTTAT
5959 CATGTATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (19 bp):
GACTTATTGGAATAAGCTA
Found at i:15431 original size:142 final size:142
Alignment explanation
Indices: 15166--15761 Score: 1012
Period size: 142 Copynumber: 4.2 Consensus size: 142
15156 TTGTAACCGT
15166 TTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGGAATCAGTGAATTGAAATCTAG
1 TTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGGAATCAGTGAATTGAAATCTAG
* * * *
15231 GCCACATTTGGACATAACTTGCGAACAAGGGTTTGTTGTAACCGTTACCTAAGGCGGTCCTCGAA
66 GCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGACGGTCCTCGAA
*
15296 CTATGTTGTCGG
131 CTATGTGGTCGG
15308 TTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGGAATCAGTGAATTGAAATCTAG
1 TTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGGAATCAGTGAATTGAAATCTAG
* *
15373 GCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTAATTAAGACGGTCCTCTAA
66 GCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGACGGTCCTCGAA
15438 CTATGTGGTCGG
131 CTATGTGGTCGG
* *
15450 TTCTAAGTGAAATGAACTTGAAACTGATGCTTACGTAGGGAAGGAATCAGTGAATTGAAATCTTG
1 TTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGGAATCAGTGAATTGAAATCTAG
* *
15515 GCCACATTTGGGCATAACTTGCAAACAAGGGTTTATTGTAACTGTTACTTAAGACGGTCCTCGAA
66 GCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGACGGTCCTCGAA
15580 CTATGTGGTCGG
131 CTATGTGGTCGG
*
15592 TTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGGAATCAGTGAATTGAAATCTTG
1 TTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGGAATCAGTGAATTGAAATCTAG
* * * *
15657 GCCACATTTGGACATTACTTGTAAACAAGGGTTTATTATAACCGTTACTTAAGATGGTCCTCGAA
66 GCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGACGGTCCTCGAA
* *
15722 CTATATGGTCAG
131 CTATGTGGTCGG
* *
15734 TTCTAAATGAAATGAACTTGTAACCGAT
1 TTCTAAGTGAAATGAACTTGAAACCGAT
15762 AAAGAACCAA
Statistics
Matches: 430, Mismatches: 24, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
142 430 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (142 bp):
TTCTAAGTGAAATGAACTTGAAACCGATGCTTACGTAGGGAAGGAATCAGTGAATTGAAATCTAG
GCCACATTTGGACATAACTTGCAAACAAGGGTTTATTGTAACCGTTACTTAAGACGGTCCTCGAA
CTATGTGGTCGG
Found at i:18424 original size:112 final size:112
Alignment explanation
Indices: 18227--18448 Score: 417
Period size: 112 Copynumber: 2.0 Consensus size: 112
18217 AAAAATTAAG
*
18227 CTCGTTTAAAATATGGATCAGATTTGAGCTTGAACATTCAAGATTCAAGTCCAACCCGATCTTTT
1 CTCGTTTAAAATATGGATCAGACTTGAGCTTGAACATTCAAGATTCAAGTCCAACCCGATCTTTT
18292 TTAAATTTATAATATTTTATGTTATGTTATTTTTATATATTATGTGA
66 TTAAATTTATAATATTTTATGTTATGTTATTTTTATATATTATGTGA
*
18339 CTCGTTTAAAATATGGATCAGACTTGAGCTTGAACATTCAAGATTCAAGTCCACCCCGATCTTTT
1 CTCGTTTAAAATATGGATCAGACTTGAGCTTGAACATTCAAGATTCAAGTCCAACCCGATCTTTT
*
18404 TTAAGTTTATAATATTTTATGTTATGTTATTTTTATATATTATGT
66 TTAAATTTATAATATTTTATGTTATGTTATTTTTATATATTATGT
18449 AATTTATAAC
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 107 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (112 bp):
CTCGTTTAAAATATGGATCAGACTTGAGCTTGAACATTCAAGATTCAAGTCCAACCCGATCTTTT
TTAAATTTATAATATTTTATGTTATGTTATTTTTATATATTATGTGA
Found at i:36484 original size:21 final size:21
Alignment explanation
Indices: 36458--36501 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
36448 TGGTTAGACC
*
36458 TAGGTTAAAAGTCAAAATCGT
1 TAGGTTAAAAGTCAAAACCGT
*
36479 TAGGTTAAGAGTCAAAACCGT
1 TAGGTTAAAAGTCAAAACCGT
36500 TA
1 TA
36502 TGTTTACCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (21 bp):
TAGGTTAAAAGTCAAAACCGT
Found at i:37670 original size:16 final size:16
Alignment explanation
Indices: 37645--37686 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
37635 ATTAATAAAT
*
37645 TTAACAATTAAAT-TA
1 TTAAAAATTAAATATA
*
37660 TTAAAATATTAATTATA
1 TTAAAA-ATTAAATATA
37677 TTAAAAATTA
1 TTAAAAATTA
37687 TGAAAAGCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 8 0.35
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAAAATTAAATATA
Found at i:43655 original size:20 final size:19
Alignment explanation
Indices: 43618--43661 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
43608 ACGTATTTAG
*
43618 TTATTTTATTATTCAGTAA
1 TTATTTTATTATTAAGTAA
43637 TATATTTCTATT-TTAAGTAA
1 T-TATTT-TATTATTAAGTAA
43657 TTATT
1 TTATT
43662 ATTTAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 5 0.23
20 13 0.59
21 4 0.18
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TTATTTTATTATTAAGTAA
Found at i:46162 original size:2 final size:2
Alignment explanation
Indices: 46155--46189 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
46145 ACCTCTGTAT
46155 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46190 TTGATTATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46298 original size:3 final size:3
Alignment explanation
Indices: 46290--46326 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
46280 AATGATAAAA
46290 ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
46327 CCGTTAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:46317 original size:8 final size:9
Alignment explanation
Indices: 46290--46326 Score: 60
Period size: 8 Copynumber: 4.3 Consensus size: 9
46280 AATGATAAAA
46290 ATTATTATT
1 ATTATTATT
46299 ATTATTATT
1 ATTATTATT
46308 ATTA-TATT
1 ATTATTATT
46316 ATTA-TATT
1 ATTATTATT
46324 ATT
1 ATT
46327 CCGTTAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 15 0.54
9 13 0.46
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTATTATT
Found at i:49696 original size:2 final size:2
Alignment explanation
Indices: 49689--49721 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
49679 ATAAAATGTT
49689 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49722 GATTAATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49786 original size:24 final size:23
Alignment explanation
Indices: 49732--49793 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
49722 GATTAATGTA
49732 AAAATAATAAAGATAATAAAATT
1 AAAATAATAAAGATAATAAAATT
* * *
49755 AAATATAATAACGATATTATAATAT
1 AAA-ATAATAAAGATAATAAAAT-T
49780 AAAATAA-AAA-ATAA
1 AAAATAATAAAGATAA
49794 ACTATCTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 3 0.09
23 5 0.16
24 20 0.62
25 4 0.12
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (23 bp):
AAAATAATAAAGATAATAAAATT
Found at i:50301 original size:2 final size:2
Alignment explanation
Indices: 50296--50331 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
50286 CTCTCTCTCT
* *
50296 CA CA CA CA CA CA CA CA CG CA CA CA CG CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
50332 AGTATATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.50, G:0.06, T:0.00
Consensus pattern (2 bp):
CA
Found at i:55097 original size:13 final size:14
Alignment explanation
Indices: 55074--55109 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
55064 ACACGAAAGT
55074 TGATATTAATTTAA
1 TGATATTAATTTAA
55088 TGAT-TTAATTTAA
1 TGATATTAATTTAA
*
55101 TGAAATTAA
1 TGATATTAA
55110 AAGTTTGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (14 bp):
TGATATTAATTTAA
Found at i:57289 original size:21 final size:20
Alignment explanation
Indices: 57263--57306 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
57253 ATCTTTTTGC
*
57263 TTTTTTGGTTCAAATCTGGGA
1 TTTTTTAGTTCAAATCT-GGA
**
57284 TTTTTTAGTTTGAATCTGGA
1 TTTTTTAGTTCAAATCTGGA
57304 TTT
1 TTT
57307 CTAAAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.18, C:0.07, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTTTTAGTTCAAATCTGGA
Found at i:57946 original size:29 final size:30
Alignment explanation
Indices: 57863--58012 Score: 130
Period size: 30 Copynumber: 5.1 Consensus size: 30
57853 AAAAACTATA
*
57863 TTTTAACCC-TAAACTTCTCTAAAAATTTAA-
1 TTTTAACCCTTAAA-TTTTCT-AAAATTTAAT
* * *
57893 ATTTAA-CCTTAAGTTTTCTAAAAATTAAT
1 TTTTAACCCTTAAATTTTCTAAAATTTAAT
*
57922 TTTTAACCCTTAAATTTTCTAAAATTTCAT
1 TTTTAACCCTTAAATTTTCTAAAATTTAAT
* * * *
57952 TTTT-GCCC-CAAACTTTCTAAAATTTCAT
1 TTTTAACCCTTAAATTTTCTAAAATTTAAT
* * * *
57980 TTTTGACCCTCAAACTTTCTAAAATTTCAT
1 TTTTAACCCTTAAATTTTCTAAAATTTAAT
58010 TTT
1 TTT
58013 GACCATCGAT
Statistics
Matches: 103, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
28 30 0.29
29 18 0.17
30 55 0.53
ACGTcount: A:0.34, C:0.19, G:0.02, T:0.45
Consensus pattern (30 bp):
TTTTAACCCTTAAATTTTCTAAAATTTAAT
Found at i:58004 original size:30 final size:30
Alignment explanation
Indices: 57907--58048 Score: 166
Period size: 30 Copynumber: 4.8 Consensus size: 30
57897 AACCTTAAGT
* * * * *
57907 TTTCTAAAAATTAATTTTTAACCCTTAAAT
1 TTTCTAAAATTTCATTTTTGACCCTCAAAC
57937 TTTCTAAAATTTCATTTTTG-CCC-CAAAC
1 TTTCTAAAATTTCATTTTTGACCCTCAAAC
57965 TTTCTAAAATTTCATTTTTGACCCTCAAAC
1 TTTCTAAAATTTCATTTTTGACCCTCAAAC
* * *
57995 TTTCTAAAATTTCA-TTTTGACCATCGATC
1 TTTCTAAAATTTCATTTTTGACCCTCAAAC
*
58024 TTTCTAAAAATTGCA-TTTTGACCCT
1 TTTCT-AAAATTTCATTTTTGACCCT
58049 TGAACTTGTT
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
28 23 0.23
29 23 0.23
30 53 0.54
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.44
Consensus pattern (30 bp):
TTTCTAAAATTTCATTTTTGACCCTCAAAC
Found at i:75355 original size:2 final size:2
Alignment explanation
Indices: 75348--75375 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
75338 CAATATTACA
75348 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75376 GTGTGTGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78886 original size:6 final size:6
Alignment explanation
Indices: 78875--78917 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
78865 TTATTTGTAC
78875 AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG A
1 AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG A
78918 TGTTTCCCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.33, T:0.16
Consensus pattern (6 bp):
AATAGG
Found at i:83428 original size:4 final size:4
Alignment explanation
Indices: 83419--83468 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
83409 CAAATAAACG
* *
83419 AGAA AGAA AGAA AGGA AG-A AGAA GAGGAA AGAA AG-A AGAA GGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA -A-GAA AGAA AGAA AGAA AGAA AGAA
83467 AG
1 AG
83469 GTAATGTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
3 6 0.15
4 28 0.72
5 2 0.05
6 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:83454 original size:17 final size:15
Alignment explanation
Indices: 83420--83468 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
83410 AAATAAACGA
83420 GAAAGAAAG-A-AAG
1 GAAAGAAAGAAGAAG
83433 G-AAG-AAGAAG-AG
1 GAAAGAAAGAAGAAG
83445 GAAAGAAAGAAGAAG
1 GAAAGAAAGAAGAAG
83460 GAAAGAAAG
1 GAAAGAAAG
83469 GTAATGTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 3 0.10
12 7 0.23
13 4 0.13
14 6 0.19
15 11 0.35
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
GAAAGAAAGAAGAAG
Done.