Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001615.1 Kokia drynarioides strain JFW-HI SEQ_113248, 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: 67896
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:3153 original size:9 final size:9
Alignment explanation
Indices: 3139--3185 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
3129 CCTCGATAGG
3139 TTCTTTTTC
1 TTCTTTTTC
*
3148 TTCTTTCTC
1 TTCTTTTTC
**
3157 TTCTTCCT-
1 TTCTTTTTC
3165 TTCTTTCTTC
1 TTCTTT-TTC
3175 TTCTTTTTC
1 TTCTTTTTC
3184 TT
1 TT
3186 GATCCTTCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 5 0.16
9 21 0.66
10 6 0.19
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:3162 original size:12 final size:11
Alignment explanation
Indices: 3144--3185 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
3134 ATAGGTTCTT
3144 TTTCTTCTTTC
1 TTTCTTCTTTC
3155 TCTTCTTCCTTTC
1 T-TTCTT-CTTTC
3168 TTTCTTC-TTC
1 TTTCTTCTTTC
3178 TTT-TTCTT
1 TTTCTTCTT
3186 GATCCTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
9 3 0.11
10 7 0.25
11 2 0.07
12 10 0.36
13 6 0.21
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTCTTCTTTC
Found at i:3173 original size:15 final size:15
Alignment explanation
Indices: 3139--3177 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
3129 CCTCGATAGG
3139 TTCTTT-TTCTT-CT
1 TTCTTTCTTCTTCCT
3152 TTC--TCTTCTTCCT
1 TTCTTTCTTCTTCCT
3165 TTCTTTCTTCTTC
1 TTCTTTCTTCTTC
3178 TTTTTCTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 1 0.05
12 5 0.23
13 8 0.36
15 8 0.36
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TTCTTTCTTCTTCCT
Found at i:3191 original size:27 final size:26
Alignment explanation
Indices: 3139--3192 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
3129 CCTCGATAGG
*
3139 TTCTTTTTCTTCTTTCTCTTCTTCCT
1 TTCTTTTTCTTCTTTCTCTTCATCCT
* *
3165 TTCTTTCTTCTTCTTTTTCTTGATCCT
1 TTCTTT-TTCTTCTTTCTCTTCATCCT
3192 T
1 T
3193 CTCCTTCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.69
Consensus pattern (26 bp):
TTCTTTTTCTTCTTTCTCTTCATCCT
Found at i:12477 original size:8 final size:8
Alignment explanation
Indices: 12466--12492 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
12456 TAAGTTACCA
12466 TTTACCCT
1 TTTACCCT
12474 TTTACCCT
1 TTTACCCT
12482 TTTACCCT
1 TTTACCCT
12490 TTT
1 TTT
12493 CTTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.33, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTACCCT
Found at i:28500 original size:12 final size:12
Alignment explanation
Indices: 28483--28507 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28473 TTTTAAGAAT
28483 TAATAGCATTCA
1 TAATAGCATTCA
28495 TAATAGCATTCA
1 TAATAGCATTCA
28507 T
1 T
28508 CATGATAACA
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:29898 original size:8 final size:8
Alignment explanation
Indices: 29885--29933 Score: 80
Period size: 8 Copynumber: 5.9 Consensus size: 8
29875 CATGCTCTCT
29885 TTTTTTTC
1 TTTTTTTC
29893 TTTTTTTC
1 TTTTTTTC
29901 TTTTTTTC
1 TTTTTTTC
29909 TTTTTTTTTC
1 --TTTTTTTC
29919 TTTTTTTC
1 TTTTTTTC
29927 TTTTTTT
1 TTTTTTT
29934 TAGCATCATT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
8 31 0.79
10 8 0.21
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTC
Found at i:29907 original size:18 final size:18
Alignment explanation
Indices: 29882--29934 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
29872 GCTCATGCTC
*
29882 TCTTTTTTT-TCTTTTTT
1 TCTTTTTTTCTTTTTTTT
29899 TCTTTTTTTCTTTTTTTT
1 TCTTTTTTTCTTTTTTTT
29917 TCTTTTTTTCTTTTTTTT
1 TCTTTTTTTCTTTTTTTT
29935 AGCATCATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 9 0.26
18 25 0.74
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (18 bp):
TCTTTTTTTCTTTTTTTT
Found at i:29919 original size:26 final size:26
Alignment explanation
Indices: 29884--29933 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
29874 TCATGCTCTC
29884 TTTTTTTTCTTTTTTTCTTTTTTTCT
1 TTTTTTTTCTTTTTTTCTTTTTTTCT
29910 TTTTTTTTCTTTTTTTCTTTTTTT
1 TTTTTTTTCTTTTTTTCTTTTTTT
29934 TAGCATCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (26 bp):
TTTTTTTTCTTTTTTTCTTTTTTTCT
Found at i:29946 original size:1 final size:1
Alignment explanation
Indices: 29884--29934 Score: 57
Period size: 1 Copynumber: 51.0 Consensus size: 1
29874 TCATGCTCTC
* * * * *
29884 TTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTTTCTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29935 AGCATCATTT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:35821 original size:2 final size:2
Alignment explanation
Indices: 35814--35843 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35804 TTAAAACGCA
35814 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
35844 GTGCTGTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36310 original size:21 final size:20
Alignment explanation
Indices: 36285--36323 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
36275 TAGCAATATT
36285 TCTTTTTCTTTTCTCTTTTTC
1 TCTTTTTCTTTTC-CTTTTTC
36306 TCTTTTTCTTTTCCTTTT
1 TCTTTTTCTTTTCCTTTT
36324 CTCATTCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (20 bp):
TCTTTTTCTTTTCCTTTTTC
Found at i:36338 original size:27 final size:27
Alignment explanation
Indices: 36283--36339 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
36273 CATAGCAATA
* * ** *
36283 TTTCTTTTTCTTTTCTCTTTTTCTCTT
1 TTTCTTTTCCTTTTCTCATTCACTATT
36310 TTTCTTTTCCTTTTCTCATTCACTATT
1 TTTCTTTTCCTTTTCTCATTCACTATT
36337 TTT
1 TTT
36340 ATAAGTGACT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTCTTTTCCTTTTCTCATTCACTATT
Found at i:45293 original size:11 final size:11
Alignment explanation
Indices: 45277--45305 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
45267 AGTAAATCAC
45277 AGTGTTGTTGA
1 AGTGTTGTTGA
45288 AGTGTTGTTGA
1 AGTGTTGTTGA
45299 AGTGTTG
1 AGTGTTG
45306 AGTATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (11 bp):
AGTGTTGTTGA
Found at i:51634 original size:16 final size:16
Alignment explanation
Indices: 51613--51643 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51603 ATACTGTGAA
51613 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
51629 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
51644 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:52514 original size:37 final size:38
Alignment explanation
Indices: 52473--52556 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 38
52463 GTACATGATC
* *
52473 ATGCAGTGACA-TTCCTGGTTGCAA-TTGAAGAATACTT
1 ATGCAGTGACAGTT-ATGGATGCAATTTGAAGAATACTT
* **
52510 ATGCAGTGATAGTTATGGATGCAATTTGAAGAATGTTT
1 ATGCAGTGACAGTTATGGATGCAATTTGAAGAATACTT
52548 ATGCAGTGA
1 ATGCAGTGA
52557 TAGTCCTAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
37 18 0.45
38 22 0.55
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (38 bp):
ATGCAGTGACAGTTATGGATGCAATTTGAAGAATACTT
Found at i:52670 original size:37 final size:37
Alignment explanation
Indices: 52595--52671 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
52585 CAATGACAAC
* **
52595 TTTAGGTGCAATCTGGAAGTGCTCATACGGGGACAGT
1 TTTAAGTGCAATCTGGAAGTGCTCATACGACGACAGT
* *
52632 TTTAAGTGCAATCTGGAAGTGCTCATGCGACGATAGT
1 TTTAAGTGCAATCTGGAAGTGCTCATACGACGACAGT
52669 TTT
1 TTT
52672 GGGCACAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.31
Consensus pattern (37 bp):
TTTAAGTGCAATCTGGAAGTGCTCATACGACGACAGT
Found at i:58475 original size:41 final size:41
Alignment explanation
Indices: 58430--58509 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
58420 TGAGTTTGAT
58430 GGGCATTCTTCGAACAGGTGCCCTTCTCCACAATAGACATA
1 GGGCATTCTTCGAACAGGTGCCCTTCTCCACAATAGACATA
* *
58471 GGGCATTCTTCGAACATGTGCCCTTCTTCACAATAGACA
1 GGGCATTCTTCGAACAGGTGCCCTTCTCCACAATAGACA
58510 CAGGCTATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (41 bp):
GGGCATTCTTCGAACAGGTGCCCTTCTCCACAATAGACATA
Found at i:65935 original size:16 final size:16
Alignment explanation
Indices: 65911--65941 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
65901 TAAAATAATC
65911 AAATAAAATAAACAAT
1 AAATAAAATAAACAAT
*
65927 AAATCAAATAAACAA
1 AAATAAAATAAACAA
65942 AGAATTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.16
Consensus pattern (16 bp):
AAATAAAATAAACAAT
Done.