Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011552.1 Kokia drynarioides strain JFW-HI SEQ_126540, 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: 84618
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 88 characters in sequence are not A, C, G, or T
Found at i:102 original size:15 final size:17
Alignment explanation
Indices: 71--107 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
61 ATTGATTATT
71 TATTTATAAAATGTTTA
1 TATTTATAAAATGTTTA
88 TATTT-TAAAAT-TTTA
1 TATTTATAAAATGTTTA
103 T-TTTA
1 TATTTA
108 ATTTTTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.16
15 5 0.26
16 6 0.32
17 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TATTTATAAAATGTTTA
Found at i:750 original size:15 final size:15
Alignment explanation
Indices: 730--762 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
720 GGAGGAGAAG
*
730 AAGAAGAAGAGAAAC
1 AAGAAGAAGAAAAAC
745 AAGAAGAAGAAAAAC
1 AAGAAGAAGAAAAAC
760 AAG
1 AAG
763 CAGGGCAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.06, G:0.24, T:0.00
Consensus pattern (15 bp):
AAGAAGAAGAAAAAC
Found at i:1546 original size:1 final size:1
Alignment explanation
Indices: 1540--1573 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
1530 AGTCCCTCTC
* *
1540 TTTTTTTTTTTCTTTTTTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1574 GTACTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:1558 original size:13 final size:12
Alignment explanation
Indices: 1538--1573 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
1528 GAAGTCCCTC
1538 TCTTTTTTTTTT
1 TCTTTTTTTTTT
1550 TCTTTTTTTTTT
1 TCTTTTTTTTTT
1562 TCTTTTTTTTTT
1 TCTTTTTTTTTT
1574 GTACTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:5863 original size:20 final size:22
Alignment explanation
Indices: 5824--5866 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
5814 TGTTGAAATA
5824 AATTTATAAATCATAATTATAAT
1 AATTTATAAA-CATAATTATAAT
5847 AATTTATAAA-A-AATTATAAT
1 AATTTATAAACATAATTATAAT
5867 TAATATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 1 0.05
23 10 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTTATAAACATAATTATAAT
Found at i:5902 original size:22 final size:24
Alignment explanation
Indices: 5842--5900 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
5832 AATCATAATT
5842 ATAATA-ATTTATAAAAAATTATAA
1 ATAATATA-TTATAAAAAATTATAA
*
5866 TTAATATATTAATAAAAAATTATTAA
1 ATAATATATT-ATAAAAAATTA-TAA
*
5892 ATAAAATAT
1 ATAATATAT
5901 AATGATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 7 0.24
25 12 0.41
26 10 0.34
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATAATATATTATAAAAAATTATAA
Found at i:5903 original size:25 final size:25
Alignment explanation
Indices: 5852--5900 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
5842 ATAATAATTT
* *
5852 ATAAAAAATTATAATTAATATATTA
1 ATAAAAAATTATAAATAAAATATTA
5877 ATAAAAAATTATTAAATAAAATAT
1 ATAAAAAATTA-TAAATAAAATAT
5901 AATGATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAAAAAATTATAAATAAAATATTA
Found at i:6841 original size:31 final size:30
Alignment explanation
Indices: 6773--6847 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
6763 CCCAAAAAAT
* *
6773 TTAAATACCAACTTAAAAAAAAATGTCAAGC
1 TTAAATACCAAATTAAAAAAAAATGTCAA-A
* **
6804 TTAAATACCAAATTAAGAAAATTTGTCAAA
1 TTAAATACCAAATTAAAAAAAAATGTCAAA
*
6834 TTCAAATATCAAAT
1 TT-AAATACCAAAT
6848 ATTATATTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 2 0.05
31 35 0.95
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.28
Consensus pattern (30 bp):
TTAAATACCAAATTAAAAAAAAATGTCAAA
Found at i:6923 original size:2 final size:2
Alignment explanation
Indices: 6918--6943 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6908 CCTTAAATTA
6918 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
6944 TCAAATTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10164 original size:8 final size:8
Alignment explanation
Indices: 10151--10180 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
10141 ATTGCACATT
10151 CTTCATGA
1 CTTCATGA
10159 CTTCATGA
1 CTTCATGA
10167 CTTCATGA
1 CTTCATGA
10175 CTTCAT
1 CTTCAT
10181 ATAATTCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.23, C:0.27, G:0.10, T:0.40
Consensus pattern (8 bp):
CTTCATGA
Found at i:13180 original size:5 final size:5
Alignment explanation
Indices: 13156--13198 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
13146 TCTATTTCAT
* * *
13156 TTTTT TTTTA TTTT- TTTTG TCTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
13199 AGGTCGTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
4 4 0.12
5 30 0.88
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (5 bp):
TTTTG
Found at i:15251 original size:3 final size:3
Alignment explanation
Indices: 15243--15281 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
15233 TGATAATCTC
15243 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
15282 CAGTGGGATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:31523 original size:22 final size:21
Alignment explanation
Indices: 31495--31542 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
31485 ATAAAATTAT
31495 TAAATATTAAAATAAAATAAAA
1 TAAATATTAAAA-AAAATAAAA
* *
31517 TAAATATTTAAAAAAATTAAA
1 TAAATATTAAAAAAAATAAAA
31538 -AAATA
1 TAAATA
31543 ATATGGACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.21
21 8 0.33
22 11 0.46
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAATATTAAAAAAAATAAAA
Found at i:33885 original size:12 final size:12
Alignment explanation
Indices: 33868--33892 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33858 CTAACAGCCC
33868 CAGTATTAGGAG
1 CAGTATTAGGAG
33880 CAGTATTAGGAG
1 CAGTATTAGGAG
33892 C
1 C
33893 CCTGATGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (12 bp):
CAGTATTAGGAG
Found at i:34278 original size:69 final size:69
Alignment explanation
Indices: 34167--34303 Score: 265
Period size: 69 Copynumber: 2.0 Consensus size: 69
34157 ATTGTATTTG
*
34167 CATTGTTATCATTTATTTATTACTTTAATATATAATGTTAGTTATATAAATTCGGTTTTAAATTC
1 CATTGTTATCATTTATTTATTACTTTAATATATAATGCTAGTTATATAAATTCGGTTTTAAATTC
34232 TTTC
66 TTTC
34236 CATTGTTATCATTTATTTATTACTTTAATATATAATGCTAGTTATATAAATTCGGTTTTAAATTC
1 CATTGTTATCATTTATTTATTACTTTAATATATAATGCTAGTTATATAAATTCGGTTTTAAATTC
34301 TTT
66 TTT
34304 TCAATTAAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.53
Consensus pattern (69 bp):
CATTGTTATCATTTATTTATTACTTTAATATATAATGCTAGTTATATAAATTCGGTTTTAAATTC
TTTC
Found at i:42489 original size:5 final size:5
Alignment explanation
Indices: 42479--42503 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42469 TCCCCCTCCT
42479 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
42504 AATATGGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:46720 original size:29 final size:31
Alignment explanation
Indices: 46651--46716 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
46641 ATATAAAAAA
*
46651 TATATATGAACTTTGATTTGATGTGCAATTG
1 TATACATGAACTTTGATTTGATGTGCAATTG
*
46682 TATACATGAACTTT-ATTTTA-GTGCAA-T-
1 TATACATGAACTTTGATTTGATGTGCAATTG
46709 TATACATG
1 TATACATG
46717 TGAAACTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 8 0.24
28 1 0.03
29 6 0.18
30 5 0.15
31 13 0.39
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (31 bp):
TATACATGAACTTTGATTTGATGTGCAATTG
Found at i:60148 original size:10 final size:9
Alignment explanation
Indices: 60122--60198 Score: 50
Period size: 9 Copynumber: 8.1 Consensus size: 9
60112 AAATTTAAAA
60122 ATAATTTTT
1 ATAATTTTT
60131 ATAATTTTT
1 ATAATTTTT
*
60140 CATATTTTTT
1 -ATAATTTTT
*
60150 A-AAATTTT
1 ATAATTTTT
*
60158 ATCGATTTTT
1 AT-AATTTTT
*
60168 A-ACTTTTT
1 ATAATTTTT
60176 AAAAATAATTTTT
1 ----ATAATTTTT
60189 ATAATTTTT
1 ATAATTTTT
60198 A
1 A
60199 AATATTAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
8 11 0.21
9 20 0.38
10 14 0.27
12 1 0.02
13 6 0.12
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (9 bp):
ATAATTTTT
Found at i:65507 original size:2 final size:2
Alignment explanation
Indices: 65500--65531 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
65490 GTTCCTACCA
65500 AT AT 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 AT AT
65532 CACCACCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65751 original size:2 final size:2
Alignment explanation
Indices: 65744--65782 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
65734 TACATTTTAA
*
65744 TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
65783 TTTTTAAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:65883 original size:21 final size:22
Alignment explanation
Indices: 65857--65899 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
65847 TATTATTATG
*
65857 AAATAAAATATTTGTT-TGAAA
1 AAATAAAAGATTTGTTATGAAA
65878 AAATAAAAGATTTGTTATGAAA
1 AAATAAAAGATTTGTTATGAAA
65900 TCTCACATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (22 bp):
AAATAAAAGATTTGTTATGAAA
Found at i:79653 original size:59 final size:57
Alignment explanation
Indices: 79590--79738 Score: 163
Period size: 59 Copynumber: 2.5 Consensus size: 57
79580 TGTTCTTAAA
* * * *
79590 TTTTAATAAGATTATTATTAAATATAATTTAATAAAAAAATAAATATTTTAATCATATT
1 TTTTAATAA-ATTATTATTAAATATAATTTAATAAAAAAACAAATAATTTAATAACA-T
** * *
79649 TTTTAACTTTATTATTATTAAATATAATTTAATAAAATAACATATAATTTAATAACAT
1 TTTTAA-TAAATTATTATTAAATATAATTTAATAAAAAAACAAATAATTTAATAACAT
*
79707 TCTTAATATAATTATTATTAAAATATGAATTT
1 TTTTAATA-AATTATTATT-AAATAT-AATTT
79739 GAGACTTTTG
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
57 1 0.01
58 15 0.20
59 53 0.71
60 6 0.08
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (57 bp):
TTTTAATAAATTATTATTAAATATAATTTAATAAAAAAACAAATAATTTAATAACAT
Done.