Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009902.1 Kokia drynarioides strain JFW-HI SEQ_124640, 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: 32212
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Warning! 43 characters in sequence are not A, C, G, or T
Found at i:930 original size:23 final size:23
Alignment explanation
Indices: 896--953 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
886 ACGCTAGCGC
*
896 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTATTTCGCACTTCGTGT
*
919 GCTTACTATTTCGCACTTTGTGT
1 GCTTACTATTTCGCACTTCGTGT
*
942 GCCTACTGATTT
1 GCTTACT-ATTT
954 GCGCTATGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 27 0.87
24 4 0.13
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (23 bp):
GCTTACTATTTCGCACTTCGTGT
Found at i:963 original size:23 final size:22
Alignment explanation
Indices: 931--1017 Score: 102
Period size: 23 Copynumber: 3.9 Consensus size: 22
921 TTACTATTTC
*
931 GCACTTTGTGTGCCTACTGATTT
1 GCACTGTGTGTGCCTACTGA-TT
* * **
954 GCGCTATGTGCACCTACTGATT
1 GCACTGTGTGTGCCTACTGATT
976 GCACTGTGTGTGCCTACTGGATT
1 GCACTGTGTGTGCCTACT-GATT
*
999 GCACTGTGTGTGCTTACTG
1 GCACTGTGTGTGCCTACTG
1018 TTTCCCCAGC
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
22 17 0.31
23 37 0.69
ACGTcount: A:0.14, C:0.23, G:0.26, T:0.37
Consensus pattern (22 bp):
GCACTGTGTGTGCCTACTGATT
Found at i:1017 original size:45 final size:47
Alignment explanation
Indices: 899--1021 Score: 116
Period size: 45 Copynumber: 2.7 Consensus size: 47
889 CTAGCGCGCT
*
899 TACTG-TTTCGCACT-TCGTGTGCTTACT-ATTTCGCACTTTGTGTGCC
1 TACTGATTT-GCACTAT-GTGTGCTTACTGATTTCGCACTGTGTGTGCC
* ** *
945 TACTGATTTGCGCTATGTGCACCTACTGA-TT-GCACTGTGTGTGCC
1 TACTGATTTGCACTATGTGTGCTTACTGATTTCGCACTGTGTGTGCC
*
990 TACTGGA-TTGCACTGTGTGTGCTTACTG-TTTC
1 TACT-GATTTGCACTATGTGTGCTTACTGATTTC
1022 CCCAGCACTT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
45 35 0.57
46 21 0.34
47 5 0.08
ACGTcount: A:0.13, C:0.24, G:0.23, T:0.41
Consensus pattern (47 bp):
TACTGATTTGCACTATGTGTGCTTACTGATTTCGCACTGTGTGTGCC
Found at i:1699 original size:14 final size:15
Alignment explanation
Indices: 1682--1714 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1672 TTTATTAGAA
*
1682 TTTATTTTCTTTAT-
1 TTTATTTACTTTATC
1696 TTTATTTACTTTATC
1 TTTATTTACTTTATC
1711 TTTA
1 TTTA
1715 AATTCAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATTTACTTTATC
Found at i:6633 original size:23 final size:23
Alignment explanation
Indices: 6580--6625 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
6570 ATTTGTTTGT
6580 AAGACATTCAGTGGTTTAAGTTG
1 AAGACATTCAGTGGTTTAAGTTG
6603 AAGACATTCAGTGGTTTAAGTTG
1 AAGACATTCAGTGGTTTAAGTTG
6626 TTGACATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (23 bp):
AAGACATTCAGTGGTTTAAGTTG
Found at i:16857 original size:6 final size:6
Alignment explanation
Indices: 16848--16874 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
16838 GGTTGCAACG
16848 GAGACT GAGACT GAGACT GAGACT GAG
1 GAGACT GAGACT GAGACT GAGACT GAG
16875 GACGCGGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.37, T:0.15
Consensus pattern (6 bp):
GAGACT
Found at i:24157 original size:30 final size:31
Alignment explanation
Indices: 24095--24161 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
24085 CTTTTTTTAC
* *
24095 CTTGAACTCGACAATTGTTCACACATTGAGG
1 CTTGAACTCGACAATTGATCACACATTAAGG
* *
24126 CTTGAACTTGACAATT-ATCTCACATTAAGG
1 CTTGAACTCGACAATTGATCACACATTAAGG
24156 CTTGAA
1 CTTGAA
24162 TTTTAAGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (31 bp):
CTTGAACTCGACAATTGATCACACATTAAGG
Found at i:24454 original size:58 final size:58
Alignment explanation
Indices: 24375--24530 Score: 163
Period size: 58 Copynumber: 2.7 Consensus size: 58
24365 CTGGGGCTTA
* ** *
24375 AAATTTTTTTGGGTCCAAGTTAGACCTCAAACTTGACAATTATTTT-CACATTAGGTCCT
1 AAATTTTTTT-GGTCTAAGTTAGACCTTGAACTTGACAATT-TTTTACACATTAGGTCCG
* * * ** *
24434 CAATTTTTTTGGTCTAAGTTAGGCTTTGAACTTGGTAATTTTTTACACATTGGGTCCG
1 AAATTTTTTTGGTCTAAGTTAGACCTTGAACTTGACAATTTTTTACACATTAGGTCCG
*
24492 AAACTTTTTTTTGTCTAAGTTAAGA-CTTGAACTTGACAA
1 AAA-TTTTTTTGGTCTAAGTT-AGACCTTGAACTTGACAA
24531 ATGTTCCCAC
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
57 4 0.05
58 36 0.46
59 36 0.46
60 2 0.03
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (58 bp):
AAATTTTTTTGGTCTAAGTTAGACCTTGAACTTGACAATTTTTTACACATTAGGTCCG
Found at i:31122 original size:2 final size:2
Alignment explanation
Indices: 31117--31152 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
31107 CCAGGGCGCG
31117 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
31153 TATATATCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.