Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007828.1 Kokia drynarioides strain JFW-HI SEQ_122464, 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: 45635
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 18 characters in sequence are not A, C, G, or T
Found at i:5233 original size:15 final size:16
Alignment explanation
Indices: 5213--5248 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5203 ATTATAAAAT
5213 ATTCAAAAT-TTTAAA
1 ATTCAAAATATTTAAA
*
5228 ATTCAAAATATTTATA
1 ATTCAAAATATTTAAA
5244 ATTCA
1 ATTCA
5249 TAAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTCAAAATATTTAAA
Found at i:5246 original size:24 final size:25
Alignment explanation
Indices: 5192--5246 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
5182 ATATCAATAA
*
5192 ATAATTTAAAAATTATAAAATATTC
1 ATAATTTAAAAATTACAAAATATTC
* * *
5217 AAAATTTTAAAATT-CAAAATATTT
1 ATAATTTAAAAATTACAAAATATTC
5241 ATAATT
1 ATAATT
5247 CATAAAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAATTTAAAAATTACAAAATATTC
Found at i:6165 original size:29 final size:29
Alignment explanation
Indices: 6103--6160 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
6093 TGGTAAAATT
**
6103 AAAATTTAGTTCTTATATTTTTATTTTTA
1 AAAATTTAGTTCTTATATTTTTAGATTTA
*
6132 AAAATTTAGTTCTTTTATTTTTTAGATTT
1 AAAATTTAGTTCTTATA-TTTTTAGATTT
6161 CAAATCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.62
Consensus pattern (29 bp):
AAAATTTAGTTCTTATATTTTTAGATTTA
Found at i:6947 original size:15 final size:17
Alignment explanation
Indices: 6915--6952 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
6905 TAGATTAAAT
6915 TGTAAAAGAGTGAAAAG
1 TGTAAAAGAGTGAAAAG
6932 TGTAAAAGA-T-AAAAG
1 TGTAAAAGAGTGAAAAG
*
6947 TATAAA
1 TGTAAA
6953 TGATTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 1 0.05
17 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.21, T:0.21
Consensus pattern (17 bp):
TGTAAAAGAGTGAAAAG
Found at i:9247 original size:22 final size:22
Alignment explanation
Indices: 9222--9277 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
9212 CATATTAGAC
* *
9222 TTTGTCTCGAGACATAAATTCT
1 TTTGTCTCGAGACATAAACTCA
* **
9244 TTTGTCTTGAGACATTCACTCA
1 TTTGTCTCGAGACATAAACTCA
9266 TTTGTCTCGAGA
1 TTTGTCTCGAGA
9278 TAGGATAACT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (22 bp):
TTTGTCTCGAGACATAAACTCA
Found at i:9345 original size:22 final size:22
Alignment explanation
Indices: 9319--9361 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
9309 AACATGACAC
* *
9319 TTTCTTGAGACATTTAAGCCTT
1 TTTCTCGAGACATATAAGCCTT
9341 TTTCTCGAGACATATAAGCCT
1 TTTCTCGAGACATATAAGCCT
9362 AGAAATGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (22 bp):
TTTCTCGAGACATATAAGCCTT
Found at i:20952 original size:28 final size:28
Alignment explanation
Indices: 20886--20970 Score: 109
Period size: 28 Copynumber: 3.0 Consensus size: 28
20876 CATAAAAAAG
* *
20886 TAAGTTGGTGGAGTCCTT-TTCCTACACAT
1 TAAGTTGGTGGAGT-CTTCTTCC-CCTCAT
*
20915 TAGGTTGGTGGAGTCTTCTTCCCCTCAT
1 TAAGTTGGTGGAGTCTTCTTCCCCTCAT
*
20943 TAAGTTGGTGGAGTCCTCTTCCCCTCAT
1 TAAGTTGGTGGAGTCTTCTTCCCCTCAT
20971 GTCCGTATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 33 0.66
29 17 0.34
ACGTcount: A:0.15, C:0.25, G:0.22, T:0.38
Consensus pattern (28 bp):
TAAGTTGGTGGAGTCTTCTTCCCCTCAT
Found at i:25523 original size:8 final size:8
Alignment explanation
Indices: 25510--25540 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
25500 TAAAATTGGA
25510 AGGTGTTG
1 AGGTGTTG
25518 AGGTGTTG
1 AGGTGTTG
25526 AGGTGTTG
1 AGGTGTTG
25534 AGGTGTT
1 AGGTGTT
25541 TGGATAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.48, T:0.39
Consensus pattern (8 bp):
AGGTGTTG
Found at i:26055 original size:16 final size:17
Alignment explanation
Indices: 26015--26056 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
26005 TTAATTATAT
*
26015 TTATTTTAATATTTTAT
1 TTATTTTAATATTTTAA
*
26032 TTA-ATTAAT-TTTTAA
1 TTATTTTAATATTTTAA
26047 TTATTTTAAT
1 TTATTTTAAT
26057 GATCTAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 8 0.38
16 10 0.48
17 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTTAATATTTTAA
Found at i:28731 original size:41 final size:41
Alignment explanation
Indices: 28644--28920 Score: 206
Period size: 41 Copynumber: 6.7 Consensus size: 41
28634 CGTTTGGATA
* * * *
28644 GAAAACGCCGCAAAAGGT-AAAGGAATAGCGGCGCTTATGG
1 GAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGG
* * *
28684 GCAAGCGCCGCTAAAGGTCAGAGCAATAACGACGCTTATGG
1 GAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGG
* * * * *
28725 GAAAGCGCCGCAAAAGGTCAAAGCAATAGCAGTGCTTATGT
1 GAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGG
* * * *
28766 GAAAGCCCCGCTAAAAGTTC--A--AA-AGCGCCGCTAAAGGTCAGAG
1 GAAAGCGCCGCT-AAAGGTCAGAGCAATAGCGGCGCT-TA--T--G-G
* * *
28809 CAATAAGTGCCGCTAAAAGTCAGAGCAATAGCGGCGCTTATGG
1 -GA-AAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGG
* * * * *
28852 GAAAGTGTCGCTCAAGGTCAGAGCAATAGCGGCGCTTTTGA
1 GAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGG
*
28893 GAAAGCGCCGCTAAAGGTCAGTGCAATA
1 GAAAGCGCCGCTAAAGGTCAGAGCAATA
28921 AGTGCCGCTA
Statistics
Matches: 182, Mismatches: 40, Indels: 29
0.73 0.16 0.12
Matches are distributed among these distances:
37 6 0.03
38 3 0.02
40 17 0.09
41 119 0.65
42 8 0.04
43 1 0.01
44 7 0.04
45 8 0.04
46 2 0.01
48 3 0.02
49 8 0.04
ACGTcount: A:0.34, C:0.21, G:0.29, T:0.16
Consensus pattern (41 bp):
GAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGG
Found at i:30999 original size:21 final size:23
Alignment explanation
Indices: 30973--31024 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
30963 ACATTACAAA
*
30973 ATATAAAAAA-T-AGAAATAAAT
1 ATATAAAAAATTCAGAAAAAAAT
30994 ATATAAAAAATTCAGAAAAAAAT
1 ATATAAAAAATTCAGAAAAAAAT
31017 ATATAAAA
1 ATATAAAA
31025 TCTAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 10 0.36
22 1 0.04
23 17 0.61
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (23 bp):
ATATAAAAAATTCAGAAAAAAAT
Found at i:31025 original size:21 final size:19
Alignment explanation
Indices: 30970--31037 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 19
30960 TACACATTAC
30970 AAAATATAAAAAAT-AGAAA
1 AAAATAT-AAAAATCAGAAA
30989 TAAATATATAAAAAATTCAGAAA
1 -AAA-ATAT-AAAAA-TCAGAAA
*
31012 AAAATATATAAAATC-TAAA
1 AAAATATA-AAAATCAGAAA
31031 AAAATAT
1 AAAATAT
31038 TGCACATTGA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
19 10 0.23
20 6 0.14
21 18 0.42
22 4 0.09
23 5 0.12
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (19 bp):
AAAATATAAAAATCAGAAA
Found at i:42800 original size:1 final size:1
Alignment explanation
Indices: 42759--42783 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
42749 CTCTTTGAAC
42759 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
42784 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.