Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005502.1 Kokia drynarioides strain JFW-HI SEQ_119566, 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: 34577
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:752 original size:21 final size:19
Alignment explanation
Indices: 728--772 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
718 CAATAAGGAC
*
728 TTCCTCCTCTCTAACAGTAAG
1 TTCCTCC-CTC-AACAGCAAG
749 TTCCT-CCTCAACAGCAAG
1 TTCCTCCCTCAACAGCAAG
767 TTCCTC
1 TTCCTC
773 TTGACCAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 13 0.59
19 3 0.14
20 1 0.05
21 5 0.23
ACGTcount: A:0.22, C:0.38, G:0.09, T:0.31
Consensus pattern (19 bp):
TTCCTCCCTCAACAGCAAG
Found at i:1699 original size:26 final size:27
Alignment explanation
Indices: 1647--1699 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1637 ACAGGTCTCT
*
1647 TTTGTCGTCTGTGATATCCTCAATGAA
1 TTTGTCGTCTATGATATCCTCAATGAA
1674 TTTGTCGTCTATGAT-TCCTCAATGAA
1 TTTGTCGTCTATGATATCCTCAATGAA
1700 CTCAGAGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.42
Consensus pattern (27 bp):
TTTGTCGTCTATGATATCCTCAATGAA
Found at i:7892 original size:19 final size:19
Alignment explanation
Indices: 7868--7906 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
7858 TTAACTTATC
7868 CTTCAATTAGCATTTAATG
1 CTTCAATTAGCATTTAATG
7887 CTTCAATTAGCATTTAATG
1 CTTCAATTAGCATTTAATG
7906 C
1 C
7907 ATTTAATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (19 bp):
CTTCAATTAGCATTTAATG
Found at i:17585 original size:30 final size:30
Alignment explanation
Indices: 17510--17643 Score: 121
Period size: 30 Copynumber: 4.4 Consensus size: 30
17500 ATTAAAATTA
* **
17510 ATCACATTAATATTAAATT-AATAAAATATT
1 ATCATATTAATATTAAATTAAATTTAATA-T
* * *
17540 ATCTAGATAAATATTAAATTAAATTTGATAT
1 ATC-ATATTAATATTAAATTAAATTTAATAT
*
17571 ATCATATTAATATTAAATT-AA-TAAATACT
1 ATCATATTAATATTAAATTAAATTTAATA-T
* *
17600 ATCTAGATAAATATTAAATTAAATTTAATAT
1 ATC-ATATTAATATTAAATTAAATTTAATAT
*
17631 TTCATATTAATAT
1 ATCATATTAATAT
17644 CTAGATAAAT
Statistics
Matches: 83, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
28 4 0.05
29 6 0.07
30 39 0.47
31 23 0.28
32 11 0.13
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (30 bp):
ATCATATTAATATTAAATTAAATTTAATAT
Found at i:17613 original size:60 final size:61
Alignment explanation
Indices: 17510--17643 Score: 225
Period size: 60 Copynumber: 2.2 Consensus size: 61
17500 ATTAAAATTA
* * *
17510 ATCACATTAATATTAAATTAATAAAATATTATCTAGATAAATATTAAATTAAATTTGATAT
1 ATCATATTAATATTAAATTAATAAAATACTATCTAGATAAATATTAAATTAAATTTAATAT
17571 ATCATATTAATATTAAATTAAT-AAATACTATCTAGATAAATATTAAATTAAATTTAATAT
1 ATCATATTAATATTAAATTAATAAAATACTATCTAGATAAATATTAAATTAAATTTAATAT
*
17631 TTCATATTAATAT
1 ATCATATTAATAT
17644 CTAGATAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
60 48 0.70
61 21 0.30
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (61 bp):
ATCATATTAATATTAAATTAATAAAATACTATCTAGATAAATATTAAATTAAATTTAATAT
Found at i:20934 original size:26 final size:26
Alignment explanation
Indices: 20905--20967 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 26
20895 ATAGAGTTTA
* *
20905 GCTCTTACGAGCCCAGACGGAATATC
1 GCTCTTACGAGCCCAAACAGAATATC
*
20931 GCTCTTACGAG-CCAAACAGAATATT
1 GCTCTTACGAGCCCAAACAGAATATC
20956 GCTCTTACGAGC
1 GCTCTTACGAGC
20968 TAGAGTTCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 22 0.67
26 11 0.33
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (26 bp):
GCTCTTACGAGCCCAAACAGAATATC
Found at i:22534 original size:13 final size:13
Alignment explanation
Indices: 22516--22540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22506 AATAAGACTC
22516 TAAAAATATTTAA
1 TAAAAATATTTAA
22529 TAAAAATATTTA
1 TAAAAATATTTA
22541 CCGTCCTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAAAATATTTAA
Found at i:24850 original size:22 final size:22
Alignment explanation
Indices: 24810--24854 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
24800 TCATATTATT
24810 TTTTATTTTTTTTAAAATATTTA
1 TTTTATTTTTTTT-AAATATTTA
24833 TTTTATTTTATTTT-AATATTTA
1 TTTTATTTT-TTTTAAATATTTA
24855 ATAATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.38
23 9 0.43
24 4 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTATTTTTTTTAAATATTTA
Found at i:25194 original size:21 final size:21
Alignment explanation
Indices: 25170--25220 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
25160 ATAATAGCAT
25170 AATCCAAATATAAAATTTAAA
1 AATCCAAATATAAAATTTAAA
* * * *
25191 AATCTAAACATAAAGTTTATA
1 AATCCAAATATAAAATTTAAA
25212 AATCCAAAT
1 AATCCAAAT
25221 TACATAATAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (21 bp):
AATCCAAATATAAAATTTAAA
Found at i:25552 original size:38 final size:38
Alignment explanation
Indices: 25501--25596 Score: 192
Period size: 38 Copynumber: 2.5 Consensus size: 38
25491 TTTCTGTTTT
25501 ATATAGTTCAGGAGAAATATTTTAGATTATTTATATGC
1 ATATAGTTCAGGAGAAATATTTTAGATTATTTATATGC
25539 ATATAGTTCAGGAGAAATATTTTAGATTATTTATATGC
1 ATATAGTTCAGGAGAAATATTTTAGATTATTTATATGC
25577 ATATAGTTCAGGAGAAATAT
1 ATATAGTTCAGGAGAAATAT
25597 CTACAACATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 58 1.00
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.40
Consensus pattern (38 bp):
ATATAGTTCAGGAGAAATATTTTAGATTATTTATATGC
Found at i:26605 original size:117 final size:117
Alignment explanation
Indices: 26399--26631 Score: 448
Period size: 117 Copynumber: 2.0 Consensus size: 117
26389 CAATTAACAT
26399 CATTATGGCTCAACTACCTTGCATTCATTGCCGATATCAGTACTATAGTTCCTCTCTTCATTAAG
1 CATTATGGCTCAACTACCTTGCATTCATTGCCGATATCAGTACTATAGTTCCTCTCTTCATTAAG
*
26464 GAATTCTTCCATATAAAGGAAAGTTTTGAAGCTTTAATTTTTTATCTGAGAC
66 GAATTCTTCCATATAAAGGAAAGTTTTGAAGCATTAATTTTTTATCTGAGAC
*
26516 CATTATGGCTCAACTAGCTTGCATTCATTGCCGATATCAGTACTATAGTTCCTCTCTTCATTAAG
1 CATTATGGCTCAACTACCTTGCATTCATTGCCGATATCAGTACTATAGTTCCTCTCTTCATTAAG
26581 GAATTCTTCCATATAAAGGAAAGTTTTGAAGCATTAATTTTTTATCTGAGA
66 GAATTCTTCCATATAAAGGAAAGTTTTGAAGCATTAATTTTTTATCTGAGA
26632 TCTTTGTTTT
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 114 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (117 bp):
CATTATGGCTCAACTACCTTGCATTCATTGCCGATATCAGTACTATAGTTCCTCTCTTCATTAAG
GAATTCTTCCATATAAAGGAAAGTTTTGAAGCATTAATTTTTTATCTGAGAC
Found at i:28207 original size:18 final size:18
Alignment explanation
Indices: 28168--28209 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
28158 GAAATAGTTA
28168 CTTAAAAATGCAATATTT
1 CTTAAAAATGCAATATTT
*
28186 -TTAAAAAT-TAAGTATTT
1 CTTAAAAATGCAA-TATTT
28203 CTTAAAA
1 CTTAAAA
28210 CATGAAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.10
17 13 0.62
18 6 0.29
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (18 bp):
CTTAAAAATGCAATATTT
Found at i:28771 original size:20 final size:20
Alignment explanation
Indices: 28735--28793 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
28725 ATAAAAAAAA
*
28735 TAAAATATTCT-TTAAAATTT
1 TAAAATATT-TATAAAAATTT
28755 TAAAATATTTATAAAAATTT
1 TAAAATATTTATAAAAATTT
***
28775 CCCAATATTTTATAAAAAT
1 TAAAATA-TTTATAAAAAT
28794 GAAAATCTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.03
20 21 0.64
21 11 0.33
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAAATATTTATAAAAATTT
Found at i:31153 original size:46 final size:46
Alignment explanation
Indices: 31061--31153 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 46
31051 CAGGGCTTAA
* * * *
31061 TATTCTTGTATTCTCGAGTCTGCAACATATGCAGGAGTTTAGAACC
1 TATTCTTGTATTCTCAAGCCTGCAACATATGCAGAAGTTGAGAACC
31107 TATTCTTGTATTCTCAAGCCTGCAACATATGCAGAAGCTTGA-AACC
1 TATTCTTGTATTCTCAAGCCTGCAACATATGCAGAAG-TTGAGAACC
31153 T
1 T
31154 TGAAAAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 39 0.93
47 3 0.07
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (46 bp):
TATTCTTGTATTCTCAAGCCTGCAACATATGCAGAAGTTGAGAACC
Done.