Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013422.1 Kokia drynarioides strain JFW-HI SEQ_128448, 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: 11252
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:947 original size:22 final size:22
Alignment explanation
Indices: 922--966 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
912 TAATATTAAC
*
922 AATTAAATTTGAAA-AGTAAAAA
1 AATTAAATTTCAAACA-TAAAAA
*
944 AATTGAATTTCAAACATAAAAA
1 AATTAAATTTCAAACATAAAAA
966 A
1 A
967 TATATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (22 bp):
AATTAAATTTCAAACATAAAAA
Found at i:5786 original size:548 final size:549
Alignment explanation
Indices: 4746--5837 Score: 1967
Period size: 548 Copynumber: 2.0 Consensus size: 549
4736 TCTAGAGAAT
*
4746 TTGAGAAAGGTTGAAAATCAATTAAAAGTAAAAAATATCAGCTATTTTCATAGTTCAACCGTTCA
1 TTGAGAAAGGTTAAAAATCAATTAAAAGTAAAAAATATCAGCTATTTTCATAGTTCAACCGTTCA
4811 TGCCATTCTCTCTTCCACCCAACTTTTGATTTTATTCCAAATAGGTCCTTCCATCATTTTTAAGC
66 TGCCATTCTCTCTTCCACCCAACTTTTGATTTTATTCCAAATAGGTCCTTCCATCATTTTTAAGC
4876 CCTCCAAGCTCCAAAATCTCCTATTTTCTTTGAAATTTCTGAAAGAAAAGTATAGAAGCGGGTTA
131 CCTCCAAGCTCCAAAATCTCCTATTTTCTTTGAAATTTCTGAAAGAAAAGTATAGAAGCGGGTTA
*
4941 GTAGACACCTCAAACTTCTTATAGAATTCATTTTGAGGTGTTAGAGAGCGTAGGGATTAAATTGA
196 GTAGACACCTCAAACTTCTTATAGAATTCATTTTGAGGTGTTAGAGAGCATAGGGATTAAATTGA
5006 GAAATTTTGAATTCAAGGGTTAAGGTAAGAAACGATTAAATTCTCATGACATACATGTATTTTAC
261 GAAATTTTGAATTCAAGGGTTAAGGTAAGAAACGATTAAATTCTCATGACATACATGTATTTTAC
5071 TGTTATTTAGCATGAAAATTATTGAATTATAGCTTATAGCTTATATGTGTTTATGTGAAATTGAA
326 TGTTATTTAGCATGAAAATTATTGAATTATAGCTTATAGCTTATATGTGTTTATGTGAAATTGAA
5136 GAGAAAGAGAAGAGAGGCAAGGATCAAATTGAAGAGAAAGGAAAAGAGAAGAGCAAAGAGTGAAA
391 GAGAAAGAGAAGAGAGGCAAGGATCAAATTGAAGAGAAAGGAAAAGAGAAGAGCAAAGAGTGAAA
* *
5201 AGAGAAGGAAATCAGCCTTTTTGTTGTAAGCACTACAAGAATTTT-AGTTTATAGTCTACATTTC
456 AGAGAAGGAAATCAGCCTTTTTGTCGTAAGCACTACAAGAATTTTGA-ATTATAGTCTA-ATTTC
*
5265 -ATAAT-ATATTTGAATTATTAGCATGGAAA
519 TATAATGATATGTGAATTATTAGCATGGAAA
*
5294 TTGAGAAAGGTTAAAAATCAATTAAAAGTAAAAAATATCAGCTCTTTTCATAGTGT-AACCGTTC
1 TTGAGAAAGGTTAAAAATCAATTAAAAGTAAAAAATATCAGCTATTTTCATAGT-TCAACCGTTC
* *
5358 ATGTCATTCTCTCTTCCATCCAACTTTTGATTTTATTCCAAATAGGTCCTTCCATCATTTTTAAG
65 ATGCCATTCTCTCTTCCACCCAACTTTTGATTTTATTCCAAATAGGTCCTTCCATCATTTTTAAG
*
5423 CCCTCCAAGCTCCAAAATCTCCTATTTTCTTTGAAATTTCTGAAAGAAAAGTATAGAAGGGGGTT
130 CCCTCCAAGCTCCAAAATCTCCTATTTTCTTTGAAATTTCTGAAAGAAAAGTATAGAAGCGGGTT
5488 AGTAGACACCTCAAACTTCTTATAGAATTCATTTTGAGGTGTTAGAGAGCATAGGGATTAAATTG
195 AGTAGACACCTCAAACTTCTTATAGAATTCATTTTGAGGTGTTAGAGAGCATAGGGATTAAATTG
* * *
5553 AGAAATTTTGAATTCAAGGGTTAAGGTAAGAAATGGTTAAATTCTCATGACATACGTGTATTTTA
260 AGAAATTTTGAATTCAAGGGTTAAGGTAAGAAACGATTAAATTCTCATGACATACATGTATTTTA
* *
5618 CTGTTATTTAGCATGAAAATTATTGAATTATAGCTTATATCTTGTATGTGTTTATGTGAAATTGA
325 CTGTTATTTAGCATGAAAATTATTGAATTATAGCTTATAGCTTATATGTGTTTATGTGAAATTGA
5683 AGAGAAAGAGAAGAGAGGCAAGGATCAAATTGAAGAGAAAGGAAAAGAGAAGAGCAAAGAGTGAA
390 AGAGAAAGAGAAGAGAGGCAAGGATCAAATTGAAGAGAAAGGAAAAGAGAAGAGCAAAGAGTGAA
* * *
5748 AAGAGAAGGAAATCAGCCTTTTTGTCGTAAGTACTACAAGAGTTTTGAATTATAGTTTAATTTCT
455 AAGAGAAGGAAATCAGCCTTTTTGTCGTAAGCACTACAAGAATTTTGAATTATAGTCTAATTTCT
*
5813 CTAATGATATGTGAATTATTAGCAT
520 ATAATGATATGTGAATTATTAGCAT
5838 AAAAATTGTT
Statistics
Matches: 522, Mismatches: 18, Indels: 7
0.95 0.03 0.01
Matches are distributed among these distances:
547 5 0.01
548 497 0.95
549 20 0.04
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (549 bp):
TTGAGAAAGGTTAAAAATCAATTAAAAGTAAAAAATATCAGCTATTTTCATAGTTCAACCGTTCA
TGCCATTCTCTCTTCCACCCAACTTTTGATTTTATTCCAAATAGGTCCTTCCATCATTTTTAAGC
CCTCCAAGCTCCAAAATCTCCTATTTTCTTTGAAATTTCTGAAAGAAAAGTATAGAAGCGGGTTA
GTAGACACCTCAAACTTCTTATAGAATTCATTTTGAGGTGTTAGAGAGCATAGGGATTAAATTGA
GAAATTTTGAATTCAAGGGTTAAGGTAAGAAACGATTAAATTCTCATGACATACATGTATTTTAC
TGTTATTTAGCATGAAAATTATTGAATTATAGCTTATAGCTTATATGTGTTTATGTGAAATTGAA
GAGAAAGAGAAGAGAGGCAAGGATCAAATTGAAGAGAAAGGAAAAGAGAAGAGCAAAGAGTGAAA
AGAGAAGGAAATCAGCCTTTTTGTCGTAAGCACTACAAGAATTTTGAATTATAGTCTAATTTCTA
TAATGATATGTGAATTATTAGCATGGAAA
Found at i:6882 original size:23 final size:23
Alignment explanation
Indices: 6757--6883 Score: 148
Period size: 23 Copynumber: 5.4 Consensus size: 23
6747 ACACTAGCGC
* *
6757 GCTCTCTGTTTAGCACATCT-CGT
1 GCTCTCTGTTTAGCAC-TGTGTGT
*
6780 GCTCTCTGTTATTAGCATTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
* *
6805 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* * *
6828 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
6851 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
6874 GCTCTCTGTT
1 GCTCTCTGTT
6884 GCCCAACACT
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
23 72 0.79
24 3 0.03
25 16 0.18
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.45
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:7819 original size:23 final size:23
Alignment explanation
Indices: 7793--7901 Score: 99
Period size: 23 Copynumber: 5.0 Consensus size: 23
7783 AGTGCTGGGC
*
7793 AATAGAGAGCACACACAGTGCTA
1 AATAGAGAGCACACAAAGTGCTA
*
7816 AATAGAGAGTACACAAA--G-T-
1 AATAGAGAGCACACAAAGTGCTA
*
7835 ACT---GAGCACACAAAGTGCT-
1 AATAGAGAGCACACAAAGTGCTA
*
7854 AATCAGAAAGCACACAAAGTGCTA
1 AAT-AGAGAGCACACAAAGTGCTA
* *
7878 AATGGAGAGCACACACAGTGCTA
1 AATAGAGAGCACACAAAGTGCTA
7901 A
1 A
7902 TCGGAGAGCG
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
16 10 0.14
18 1 0.01
19 5 0.07
20 1 0.01
21 1 0.01
23 48 0.70
24 3 0.04
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (23 bp):
AATAGAGAGCACACAAAGTGCTA
Found at i:7853 original size:39 final size:39
Alignment explanation
Indices: 7799--7873 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
7789 GGGCAATAGA
* * *
7799 GAGCACACACAGTGCTAAAT-AGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCT-AATCAGAAAGCACACAAAGTACT
7838 GAGCACACAAAGTGCTAATCAGAAAGCACACAAAGT
1 GAGCACACAAAGTGCTAATCAGAAAGCACACAAAGT
7874 GCTAAATGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 3 0.09
39 29 0.91
ACGTcount: A:0.45, C:0.21, G:0.20, T:0.13
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAATCAGAAAGCACACAAAGTACT
Found at i:7914 original size:25 final size:23
Alignment explanation
Indices: 7838--7910 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
7828 ACAAAGTACT
*
7838 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCGGA
*
7861 AAGCACACAAAGTGCTAAAT-GGA
1 GAGCACACAAAGTGCT-AATCGGA
*
7884 GAGCACACACAGTGCTAATCGGA
1 GAGCACACAAAGTGCTAATCGGA
7907 GAGC
1 GAGC
7911 GCACTAGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.07
23 38 0.86
24 3 0.07
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCGGA
Found at i:10004 original size:14 final size:14
Alignment explanation
Indices: 9985--10025 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
9975 ACAATAGATT
9985 TTTAATTAAATAAA
1 TTTAATTAAATAAA
**
9999 TTTAATTACTTAAA
1 TTTAATTAAATAAA
10013 TTTAATTAAATAA
1 TTTAATTAAATAA
10026 GATGCAACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (14 bp):
TTTAATTAAATAAA
Done.