Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005124.1 Kokia drynarioides strain JFW-HI SEQ_118955, 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: 18151
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.35
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:914 original size:42 final size:43
Alignment explanation
Indices: 861--1071 Score: 196
Period size: 43 Copynumber: 5.0 Consensus size: 43
851 TTTGTTAATG
* *
861 TTAGTGGTGTTTGTGGAAAAAGCGTCGTTAAAGATCATG-TTT
1 TTAGCGGTGTTTGTGGAAAAAGCGTCGCTAAAGATCATGTTTT
* * * *
903 TTAGCAGTGTTTGTGGGATAAA-CGTCGTTAAAGATTATGTTTT
1 TTAGCGGTGTTTGT-GGAAAAAGCGTCGCTAAAGATCATGTTTT
* * * * *
946 TTAGCGGCGTTTGTGGGATAAGCGTTGCTAAAGATCGTGTTTT
1 TTAGCGGTGTTTGTGGAAAAAGCGTCGCTAAAGATCATGTTTT
* * * * *
989 TTAGCGGGGTTTAT-GAGATAAGCGTTGCTAAAGACCATGTTTT
1 TTAGCGGTGTTTGTGGA-AAAAGCGTCGCTAAAGATCATGTTTT
* * **
1032 TTAGCGGAGTTTTTGG-AAAAGCACCGCTAAAGATCATGTT
1 TTAGCGGTGTTTGTGGAAAAAGCGTCGCTAAAGATCATGTT
1072 CTATAACGAC
Statistics
Matches: 139, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
42 52 0.37
43 86 0.62
44 1 0.01
ACGTcount: A:0.25, C:0.10, G:0.28, T:0.36
Consensus pattern (43 bp):
TTAGCGGTGTTTGTGGAAAAAGCGTCGCTAAAGATCATGTTTT
Found at i:1587 original size:33 final size:33
Alignment explanation
Indices: 1550--1800 Score: 118
Period size: 33 Copynumber: 7.5 Consensus size: 33
1540 ATAACCTGAT
* * *
1550 TATGGTCTTAACATCATAATGTCATAGTCCAAC
1 TATGGTCTTAACATCAGAATGCCATAGCCCAAC
* * *
1583 TATGGTCTTATCATTAGAATGCCATAGCCCAGC
1 TATGGTCTTAACATCAGAATGCCATAGCCCAAC
* * * *
1616 TATGGTCTT-ACATCTATATACACTGCCATGGTCCACC
1 TATGGTCTTAACATC---AGA-A-TGCCATAGCCCAAC
* * * *
1653 CACGGTCTT-ACGTCAGAATACCATAGCCCAAC
1 TATGGTCTTAACATCAGAATGCCATAGCCCAAC
* * * *
1685 TATGGTCAT-ACATCTATATACACTGCCATGGTCCAAC
1 TATGGTCTTAACATC---AGA-A-TGCCATAGCCCAAC
* * * * *
1722 CATGGTCTT-AC-GCTAGAATGTCATAGCACAGC
1 TATGGTCTTAACATC-AGAATGCCATAGCCCAAC
* * * *
1754 TATGGCCTTATCATTAGAATGCCATAGCCCAGC
1 TATGGTCTTAACATCAGAATGCCATAGCCCAAC
1787 TATGGTCTT-ACATC
1 TATGGTCTTAACATC
1801 TATATACATT
Statistics
Matches: 159, Mismatches: 47, Indels: 25
0.69 0.20 0.11
Matches are distributed among these distances:
32 42 0.26
33 63 0.40
34 5 0.03
35 4 0.03
36 3 0.02
37 42 0.26
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (33 bp):
TATGGTCTTAACATCAGAATGCCATAGCCCAAC
Found at i:1660 original size:37 final size:37
Alignment explanation
Indices: 1617--1732 Score: 116
Period size: 37 Copynumber: 3.3 Consensus size: 37
1607 TAGCCCAGCT
*
1617 ATGGTCTTACATCTATATACACTGCCATGGTCCACCC
1 ATGGTCTTACATCTATATACACTGCCATGGTCCAACC
* * * * * * *
1654 ACGGTCTTACGTC---AGA-A-TACCATAGCCCAACT
1 ATGGTCTTACATCTATATACACTGCCATGGTCCAACC
*
1686 ATGGTCATACATCTATATACACTGCCATGGTCCAACC
1 ATGGTCTTACATCTATATACACTGCCATGGTCCAACC
1723 ATGGTCTTAC
1 ATGGTCTTAC
1733 GCTAGAATGT
Statistics
Matches: 57, Mismatches: 17, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
32 20 0.35
33 1 0.02
34 2 0.04
35 2 0.04
36 1 0.02
37 31 0.54
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (37 bp):
ATGGTCTTACATCTATATACACTGCCATGGTCCAACC
Found at i:1679 original size:69 final size:69
Alignment explanation
Indices: 1597--1763 Score: 246
Period size: 69 Copynumber: 2.4 Consensus size: 69
1587 GTCTTATCAT
*
1597 TAGAATGCCATAGCCCAGCTATGGTCTTACATCTATATACACTGCCATGGTCCACCCACGGTCTT
1 TAGAATGCCATAGCCCAGCTATGGTCTTACATCTATATACACTGCCATGGTCCAACCACGGTCTT
1662 ACG-
66 ACGC
* * * *
1665 TCAGAATACCATAGCCCAACTATGGTCATACATCTATATACACTGCCATGGTCCAACCATGGTCT
1 T-AGAATGCCATAGCCCAGCTATGGTCTTACATCTATATACACTGCCATGGTCCAACCACGGTCT
1730 TACGC
65 TACGC
* * *
1735 TAGAATGTCATAGCACAGCTATGGCCTTA
1 TAGAATGCCATAGCCCAGCTATGGTCTTA
1764 TCATTAGAAT
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
68 1 0.01
69 84 0.98
70 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (69 bp):
TAGAATGCCATAGCCCAGCTATGGTCTTACATCTATATACACTGCCATGGTCCAACCACGGTCTT
ACGC
Found at i:12736 original size:11 final size:11
Alignment explanation
Indices: 12720--12772 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
12710 CAAGTCAAAC
12720 CGTTGACCGAT
1 CGTTGACCGAT
12731 CGTTGACCGGAT
1 CGTTGACC-GAT
*
12743 -GTTGACCGAA
1 CGTTGACCGAT
* * *
12753 CATTGATCGAC
1 CGTTGACCGAT
12764 CGTTGACCG
1 CGTTGACCG
12773 TTGACCATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 2 0.06
11 29 0.85
12 3 0.09
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.25
Consensus pattern (11 bp):
CGTTGACCGAT
Found at i:12773 original size:7 final size:7
Alignment explanation
Indices: 12761--12852 Score: 62
Period size: 7 Copynumber: 13.4 Consensus size: 7
12751 AACATTGATC
12761 GACCGTT
1 GACCGTT
12768 GACCGTT
1 GACCGTT
*
12775 GACCATT
1 GACCGTT
12782 GACCGTT
1 GACCGTT
**
12789 GA-TTTT
1 GACCGTT
*
12795 GACTGTT
1 GACCGTT
*
12802 AACCGTT
1 GACCGTT
* ***
12809 AATAATT
1 GACCGTT
*
12816 GACCATT
1 GACCGTT
12823 GACCGTT
1 GACCGTT
*
12830 AACCGTT
1 GACCGTT
*
12837 GA-CTTT
1 GACCGTT
12843 GACCGTT
1 GACCGTT
12850 GAC
1 GAC
12853 TTTTTTCGAA
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
6 9 0.14
7 56 0.86
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.34
Consensus pattern (7 bp):
GACCGTT
Found at i:12849 original size:13 final size:13
Alignment explanation
Indices: 12831--12855 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12821 TTGACCGTTA
12831 ACCGTTGACTTTG
1 ACCGTTGACTTTG
12844 ACCGTTGACTTT
1 ACCGTTGACTTT
12856 TTTCGAAAAA
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:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (13 bp):
ACCGTTGACTTTG
Found at i:17099 original size:31 final size:32
Alignment explanation
Indices: 17061--17120 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
17051 TACATTTCAG
17061 TCCCTCAA-ATTTGAAAATGTGACAAAAACAA
1 TCCCTCAACATTTGAAAATGTGACAAAAACAA
*
17092 TCCCTCAACTTTTGAAAATGTGACAAAAA
1 TCCCTCAACATTTGAAAATGTGACAAAAA
17121 AGTCCTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 8 0.30
32 19 0.70
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (32 bp):
TCCCTCAACATTTGAAAATGTGACAAAAACAA
Found at i:17256 original size:30 final size:31
Alignment explanation
Indices: 17215--17281 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
17205 ATTACGTTTA
* * * *
17215 ACAAAATAGTCACTCAACTT-TGGAAATGTG
1 ACAAAACAGTCACTAAACTTATCGAAAAGTG
*
17245 ACAAAACAGTCACTAAAGTTATCGAAAAGTG
1 ACAAAACAGTCACTAAACTTATCGAAAAGTG
17276 ACAAAA
1 ACAAAA
17282 TAATCCTCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.21
Consensus pattern (31 bp):
ACAAAACAGTCACTAAACTTATCGAAAAGTG
Done.