Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013167.1 Kokia drynarioides strain JFW-HI SEQ_128186, 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: 37236
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:4725 original size:16 final size:16
Alignment explanation
Indices: 4679--4725 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
4669 TTAAATTATT
4679 TATATTGTTTTATTTTA
1 TATATT-TTTTATTTTA
* *
4696 -ATATTTAATAATTTTA
1 TATATTT-TTTATTTTA
4712 TATATTTTTTATTT
1 TATATTTTTTATTT
4726 ATTAAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATTTTA
Found at i:17329 original size:13 final size:14
Alignment explanation
Indices: 17295--17323 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17285 TTCGTGGTCT
17295 TTAGTTAA-TTTAA
1 TTAGTTAATTTTAA
17308 TTAGTTAATTTTAA
1 TTAGTTAATTTTAA
17322 TT
1 TT
17324 TTTAATCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTAGTTAATTTTAA
Found at i:19660 original size:12 final size:12
Alignment explanation
Indices: 19601--19661 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
19591 GAGTAGGATA
* *
19601 TGTATCTATATA
1 TGTATCTGTATC
*
19613 TGTATTTGTATC
1 TGTATCTGTATC
* * *
19625 TATATATGTATT
1 TGTATCTGTATC
*
19637 TGTATCTATATC
1 TGTATCTGTATC
19649 TGTATCTGTATC
1 TGTATCTGTATC
19661 T
1 T
19662 ATATTTATGT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.25, C:0.10, G:0.11, T:0.54
Consensus pattern (12 bp):
TGTATCTGTATC
Found at i:19675 original size:36 final size:36
Alignment explanation
Indices: 19601--19678 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
19591 GAGTAGGATA
* *
19601 TGTATCTATATATGTATTTGTATCTATATATGTATT
1 TGTATCTATATATGTATCTGTATCTATATATATATT
* * *
19637 TGTATCTATATCTGTATCTGTATCTATATTTATGTT
1 TGTATCTATATATGTATCTGTATCTATATATATATT
19673 TGTATC
1 TGTATC
19679 AGCATCTGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (36 bp):
TGTATCTATATATGTATCTGTATCTATATATATATT
Found at i:19678 original size:18 final size:18
Alignment explanation
Indices: 19601--19665 Score: 112
Period size: 18 Copynumber: 3.6 Consensus size: 18
19591 GAGTAGGATA
19601 TGTATCTATATATGTATT
1 TGTATCTATATATGTATT
19619 TGTATCTATATATGTATT
1 TGTATCTATATATGTATT
* *
19637 TGTATCTATATCTGTATC
1 TGTATCTATATATGTATT
19655 TGTATCTATAT
1 TGTATCTATAT
19666 TTATGTTTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (18 bp):
TGTATCTATATATGTATT
Found at i:19685 original size:24 final size:24
Alignment explanation
Indices: 19649--19702 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
19639 TATCTATATC
* * *
19649 TGTATCTGTATCTAT-ATTTATGTT
1 TGTATCAGCATCTATAATTT-TATT
*
19673 TGTATCAGCATCTGTAATTTTATT
1 TGTATCAGCATCTATAATTTTATT
19697 TGTATC
1 TGTATC
19703 TAAACTACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.54
Consensus pattern (24 bp):
TGTATCAGCATCTATAATTTTATT
Found at i:19686 original size:36 final size:36
Alignment explanation
Indices: 19601--19688 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 36
19591 GAGTAGGATA
* * * *
19601 TGTATCTATATATGTATTTGTATCTATATATGTATT
1 TGTATCTACATCTGTATCTGTATCTATATATATATT
* * *
19637 TGTATCTATATCTGTATCTGTATCTATATTTATGTT
1 TGTATCTACATCTGTATCTGTATCTATATATATATT
19673 TGTATC-AGCATCTGTA
1 TGTATCTA-CATCTGTA
19689 ATTTTATTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 1 0.02
36 44 0.98
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.52
Consensus pattern (36 bp):
TGTATCTACATCTGTATCTGTATCTATATATATATT
Found at i:19995 original size:33 final size:33
Alignment explanation
Indices: 19958--20038 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
19948 GTTTGGGTTT
19958 TCTGTTAGATTTTTAGTTAAATGGTTTAGAAAG
1 TCTGTTAGATTTTTAGTTAAATGGTTTAGAAAG
*
19991 TCTGTTTGATTTTTAGTTAAATGGTTTAGAAAG
1 TCTGTTAGATTTTTAGTTAAATGGTTTAGAAAG
* * *
20024 TTTATTCGATTTTTA
1 TCTGTTAGATTTTTA
20039 CAAATTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.27, C:0.04, G:0.19, T:0.51
Consensus pattern (33 bp):
TCTGTTAGATTTTTAGTTAAATGGTTTAGAAAG
Found at i:23338 original size:24 final size:25
Alignment explanation
Indices: 23275--23338 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 25
23265 TCTTCTAAGC
23275 ATTTTAA-T-ATGTATTTTTTATTTA
1 ATTTTAATTAATGT-TTTTTTATTTA
* *
23299 ATGTTATTTCAA-GTTTTTTTA-TTA
1 ATTTTAATT-AATGTTTTTTTATTTA
23323 ATTTTAATTAATGTTT
1 ATTTTAATTAATGTTT
23339 ATAATACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
23 2 0.06
24 19 0.59
25 8 0.25
26 2 0.06
27 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (25 bp):
ATTTTAATTAATGTTTTTTTATTTA
Found at i:26871 original size:16 final size:17
Alignment explanation
Indices: 26841--26872 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
26831 CAAAATGTTT
26841 AAATTATATATTTTAAA
1 AAATTATATATTTTAAA
26858 AAATTATA-ATTTTAA
1 AAATTATATATTTTAA
26873 TTACAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTATATATTTTAAA
Found at i:28995 original size:20 final size:20
Alignment explanation
Indices: 28953--28995 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
28943 CTAAATAAAC
* *
28953 AAACACAAATCTAATCTTCA
1 AAACACAAATATAATCTTAA
* *
28973 AAACATAAATATAATGTTAA
1 AAACACAAATATAATCTTAA
28993 AAA
1 AAA
28996 TTATATCTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (20 bp):
AAACACAAATATAATCTTAA
Found at i:29035 original size:18 final size:19
Alignment explanation
Indices: 28989--29036 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
28979 AAATATAATG
28989 TTAAAAATTATATCTAAAAA
1 TTAAAAA-TATATCTAAAAA
*
29009 TTAACAATA-ATCT-AAAA
1 TTAAAAATATATCTAAAAA
29026 TATAAAAATAT
1 T-TAAAAATAT
29037 TTTTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 5 0.21
18 11 0.46
19 2 0.08
20 6 0.25
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAAAATATATCTAAAAA
Found at i:32298 original size:55 final size:55
Alignment explanation
Indices: 32195--32305 Score: 179
Period size: 55 Copynumber: 2.0 Consensus size: 55
32185 TCTAGAAAAA
**
32195 CCTTCCGCACATATAAGGAACAAATACGGGCTTAGTGGATCTTTTTGTCTCAATC
1 CCTTCCGCACATATAAGGAACAAATACGGGCTTAGTGGATCTCCTTGTCTCAATC
*
32250 CCTTCCGCACATATAAGGAACGAATACGGGCTTAGTGGAT-TCCCTTGTCTCAATC
1 CCTTCCGCACATATAAGGAACAAATACGGGCTTAGTGGATCT-CCTTGTCTCAATC
32305 C
1 C
32306 TCTTGACGGT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 1 0.02
55 51 0.98
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (55 bp):
CCTTCCGCACATATAAGGAACAAATACGGGCTTAGTGGATCTCCTTGTCTCAATC
Done.