Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012897.1 Kokia drynarioides strain JFW-HI SEQ_127911, 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: 7423
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Found at i:1701 original size:18 final size:18
Alignment explanation
Indices: 1678--1897 Score: 87
Period size: 18 Copynumber: 11.9 Consensus size: 18
1668 TGATGAATAA
1678 ATATTTAATTAAATAATT
1 ATATTTAATTAAATAATT
**
1696 ATATTTAATTATTTAA-T
1 ATATTTAATTAAATAATT
*
1713 -TATTTAATTATATTTAATT
1 ATATTTAATTA-A-ATAATT
*
1732 AAATATTTAATTATAA-ACAGT
1 --ATATTTAATTA-AATA-ATT
*
1753 ATCAGTTAATATATACA-AATT
1 AT-ATTTAAT-TA-A-ATAATT
* * *
1774 -TATTTGA-TGAATGA--
1 ATATTTAATTAAATAATT
1788 ATATTTAATTAAATAATT
1 ATATTTAATTAAATAATT
** *
1806 ATATTTAATTATTTATTT
1 ATATTTAATTAAATAATT
*** **
1824 ATAAACAGTATTAGTTAATT
1 ATATTTA--ATTAAATAATT
1844 AAATATTTAATTAAATAATT
1 --ATATTTAATTAAATAATT
**
1864 ATATTTAATTATTTAATT
1 ATATTTAATTAAATAATT
*
1882 ATGTTTAATTAAATAA
1 ATATTTAATTAAATAA
1898 ACAATATTTA
Statistics
Matches: 151, Mismatches: 32, Indels: 38
0.68 0.14 0.17
Matches are distributed among these distances:
15 7 0.05
16 17 0.11
17 2 0.01
18 66 0.44
19 7 0.05
20 26 0.17
21 8 0.05
22 18 0.12
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (18 bp):
ATATTTAATTAAATAATT
Found at i:1708 original size:8 final size:8
Alignment explanation
Indices: 1697--1745 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
1687 TAAATAATTA
1697 TATTTAAT
1 TATTTAAT
1705 TATTTAAT
1 TATTTAAT
1713 TATTTAAT
1 TATTTAAT
*
1721 TA--TATT
1 TATTTAAT
* *
1727 TAATTAAA
1 TATTTAAT
1735 TATTTAAT
1 TATTTAAT
1743 TAT
1 TAT
1746 AAACAGTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
6 5 0.15
8 29 0.85
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTTAAT
Found at i:1872 original size:110 final size:110
Alignment explanation
Indices: 1649--1856 Score: 335
Period size: 110 Copynumber: 1.9 Consensus size: 110
1639 TGCGATTTGA
*
1649 TAATATATACAAATTTCTTTGATGAATAAATATTTAATTAAATAATTATATTTAATTATTTAATT
1 TAATATATACAAATTTATTTGATGAATAAATATTTAATTAAATAATTATATTTAATTATTTAATT
** * *
1714 ATTTAATTATATTTAATTAAATATTTAATTATAAACAGTATCAGT
66 ATAAAAGTATAGTTAATTAAATATTTAATTATAAACAGTATCAGT
* *
1759 TAATATATACAAATTTATTTGATGAATGAATATTTAATTAAATAATTATATTTAATTATTTATTT
1 TAATATATACAAATTTATTTGATGAATAAATATTTAATTAAATAATTATATTTAATTATTTAATT
1824 ATAAACAGTATTAGTTAATTAAATATTTAATTA
66 ATAAA-AGTA-TAGTTAATTAAATATTTAATTA
1857 AATAATTATA
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
110 65 0.73
111 3 0.03
112 21 0.24
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (110 bp):
TAATATATACAAATTTATTTGATGAATAAATATTTAATTAAATAATTATATTTAATTATTTAATT
ATAAAAGTATAGTTAATTAAATATTTAATTATAAACAGTATCAGT
Found at i:1874 original size:10 final size:10
Alignment explanation
Indices: 1846--1933 Score: 69
Period size: 10 Copynumber: 9.3 Consensus size: 10
1836 AGTTAATTAA
1846 ATATTTAATT
1 ATATTTAATT
*
1856 A-A-ATAATT
1 ATATTTAATT
1864 ATATTTAA-T
1 ATATTTAATT
1873 -TATTTAATT
1 ATATTTAATT
*
1882 ATGTTTAATT
1 ATATTTAATT
* * **
1892 A-AATAAACA
1 ATATTTAATT
*
1901 ATATTTAATC
1 ATATTTAATT
1911 ATATTTAATT
1 ATATTTAATT
*
1921 ATTTTTAATT
1 ATATTTAATT
1931 ATA
1 ATA
1934 AAAAACAATC
Statistics
Matches: 58, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
8 13 0.22
9 8 0.14
10 37 0.64
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (10 bp):
ATATTTAATT
Found at i:3997 original size:43 final size:42
Alignment explanation
Indices: 3949--4216 Score: 315
Period size: 43 Copynumber: 6.3 Consensus size: 42
3939 ATCTGTTAAT
*
3949 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTAT-GGGAAAGCGCCGCTAAAGACCATGTTC
*
3992 TTTAGCGGCGTTTATGGGAGAAGCACCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTATGGGA-AAGCGCCGCTAAAGACCATGTTC
* *
4035 TTTAGCGGCGTTTATTGGAAAAGTGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTA-TGGGAAAGCGCCGCTAAAGACCATGTTC
* * *
4078 TTTAGCGGTGCTTATGGGAAAGGTGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTATGGGAAA-GCGCCGCTAAAGACCATGTTC
* * * * * * * *
4121 -TT-GAGGCGTTTGTTGTAGAAGTGTCGGTAAAGACCACGTTC
1 TTTAGCGGCGTTTATGGGA-AAGCGCCGCTAAAGACCATGTTC
* * *
4162 TTTAGCGGCGTTTGTGGGGAAGCGCCGCTAAAGACCATGCTC
1 TTTAGCGGCGTTTATGGGAAAGCGCCGCTAAAGACCATGTTC
4204 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
4217 TTCCTCATAA
Statistics
Matches: 193, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
41 27 0.14
42 47 0.24
43 115 0.60
44 4 0.02
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.28
Consensus pattern (42 bp):
TTTAGCGGCGTTTATGGGAAAGCGCCGCTAAAGACCATGTTC
Found at i:4094 original size:86 final size:86
Alignment explanation
Indices: 3949--4216 Score: 355
Period size: 86 Copynumber: 3.2 Consensus size: 86
3939 ATCTGTTAAT
* * *
3949 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTATGGGAGAA
1 TTTAGCGGCGTTTGTTGGAAAAGTGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTATGGGAGAA
*
4014 GCACCGCTAAAGACCATGTTC
66 GCGCCGCTAAAGACCATGTTC
* * *
4035 TTTAGCGGCGTTTATTGGAAAAGTGCCGCTAAAGACCATGTTCTTTAGCGGTGCTTATGGGA-AA
1 TTTAGCGGCGTTTGTTGGAAAAGTGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTATGGGAGAA
*
4099 GGTGCCGCTAAAGACCATGTTC
66 -GCGCCGCTAAAGACCATGTTC
* * * * * * *
4121 -TT-GAGGCGTTTGTTGTAGAAGTGTCGGTAAAGACCACGTTCTTTAGCGGCGTTTGTGGG-GAA
1 TTTAGCGGCGTTTGTTGGAAAAGTGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTATGGGAGAA
*
4183 GCGCCGCTAAAGACCATGCTC
66 GCGCCGCTAAAGACCATGTTC
4204 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
4217 TTCCTCATAA
Statistics
Matches: 157, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
83 19 0.12
84 51 0.32
85 12 0.08
86 75 0.48
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.28
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTTGGAAAAGTGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTATGGGAGAA
GCGCCGCTAAAGACCATGTTC
Found at i:6292 original size:21 final size:21
Alignment explanation
Indices: 6268--6307 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6258 AAAAATTTTC
* *
6268 AATTTGAGTTGAGTGAAATGA
1 AATTCGAGTTGAGTCAAATGA
6289 AATTCGAGTTGAGTCAAAT
1 AATTCGAGTTGAGTCAAAT
6308 AAAGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.33
Consensus pattern (21 bp):
AATTCGAGTTGAGTCAAATGA
Found at i:6581 original size:10 final size:10
Alignment explanation
Indices: 6526--6583 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
6516 ATATTAAATT
**
6526 TTTTTTATCT
1 TTTTTTATAA
6536 TTTTTTATATA
1 TTTTTTATA-A
* *
6547 TTCTTTAGAA
1 TTTTTTATAA
*
6557 TTCTTTATAA
1 TTTTTTATAA
6567 TTTTTTTATAA
1 -TTTTTTATAA
6578 TTTTTT
1 TTTTTT
6584 TTAAAAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 24 0.60
11 16 0.40
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:6586 original size:12 final size:11
Alignment explanation
Indices: 6525--6584 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
6515 TATATTAAAT
*
6525 TTTTTTTAT-C
1 TTTTTTTATAA
6535 TTTTTTTAT-A
1 TTTTTTTATAA
* *
6545 TATTCTTTAGAA
1 T-TTTTTTATAA
*
6557 -TTCTTTATAA
1 TTTTTTTATAA
6567 TTTTTTTATAA
1 TTTTTTTATAA
6578 TTTTTTT
1 TTTTTTT
6585 TAAAAATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
10 19 0.45
11 22 0.52
12 1 0.02
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTTTTTATAA
Done.