Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010674.1 Kokia drynarioides strain JFW-HI SEQ_125620, 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: 3062
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:302 original size:10 final size:10
Alignment explanation
Indices: 287--316 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
277 GGACCAAGTT
287 CCGACCCAAC
1 CCGACCCAAC
*
297 CCGACCCAAT
1 CCGACCCAAC
307 CCGACCCAAC
1 CCGACCCAAC
317 TCAGGNGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.30, C:0.57, G:0.10, T:0.03
Consensus pattern (10 bp):
CCGACCCAAC
Found at i:429 original size:134 final size:133
Alignment explanation
Indices: 189--455 Score: 516
Period size: 134 Copynumber: 2.0 Consensus size: 133
179 ATGAAAAAAA
189 GGGGTATTAGATAACTTTTATAGCATATCGAAATGACATCGTGTTGGTCTCGGCCCTTAAACCCC
1 GGGGTATTAGATAACTTTTATAGCATATCGAAATGACATCGTGTTGGTCTCGGCCCTTAAACCCC
*
254 AAAATGGTGCCGTTTCACCTCAAGGACCAAGTTCCGACCCAACCCGACCCAATCCGACCCAACTC
66 AAAACGGTGCCGTTTCACCTCAAGGACCAAGTTCCGACCCAACCCGACCCAATCCGACCCAACTC
319 AGG
131 AGG
322 NGGGGTATTAGATAACTTTTATAGCATATCGAAATGACATCGTGTTGGTCTCGGCCCTTAAACCC
1 -GGGGTATTAGATAACTTTTATAGCATATCGAAATGACATCGTGTTGGTCTCGGCCCTTAAACCC
387 CAAAACGGTGCCGTTTCACCTCAAGGACCAAGTTCCGACCCAACCCGACCCAATCCGACCCAACT
65 CAAAACGGTGCCGTTTCACCTCAAGGACCAAGTTCCGACCCAACCCGACCCAATCCGACCCAACT
452 CAGG
130 CAGG
456 ATCCGCGTGT
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 132 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.22
Consensus pattern (133 bp):
GGGGTATTAGATAACTTTTATAGCATATCGAAATGACATCGTGTTGGTCTCGGCCCTTAAACCCC
AAAACGGTGCCGTTTCACCTCAAGGACCAAGTTCCGACCCAACCCGACCCAATCCGACCCAACTC
AGG
Found at i:436 original size:10 final size:10
Alignment explanation
Indices: 421--450 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
411 GGACCAAGTT
421 CCGACCCAAC
1 CCGACCCAAC
*
431 CCGACCCAAT
1 CCGACCCAAC
441 CCGACCCAAC
1 CCGACCCAAC
451 TCAGGATCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.30, C:0.57, G:0.10, T:0.03
Consensus pattern (10 bp):
CCGACCCAAC
Found at i:965 original size:29 final size:29
Alignment explanation
Indices: 863--954 Score: 123
Period size: 30 Copynumber: 3.1 Consensus size: 29
853 TGAAGTCTTC
863 AAAATTACATTTTTACCCTTAAATTTTCCA
1 AAAATTACATTTTTACCC-TAAATTTTCCA
* **
893 AAAATTTCATTTTTAACCCTAACCTTTCCA
1 AAAATTACATTTTT-ACCCTAAATTTTCCA
923 AAAATTACA-TTTTACTCCTAAATTTTCCA
1 AAAATTACATTTTTAC-CCTAAATTTTCCA
952 AAA
1 AAA
955 TTCTATTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
28 2 0.04
29 18 0.33
30 30 0.56
31 4 0.07
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (29 bp):
AAAATTACATTTTTACCCTAAATTTTCCA
Found at i:991 original size:29 final size:29
Alignment explanation
Indices: 862--992 Score: 78
Period size: 30 Copynumber: 4.5 Consensus size: 29
852 ATGAAGTCTT
**
862 CAAAATTA-CATTTTT-ACCCTTAAATTTTC
1 CAAAATTACCATTTTTAACCC--AAACCTTC
* *
891 CAAAAATT-TCATTTTTAACCCTAACCTTTC
1 C-AAAATTACCATTTTTAACCCAAACC-TTC
**
921 CAAAAATTA-CA-TTTT-ACTCCTAAATTTTC
1 C-AAAATTACCATTTTTAAC-CC-AAACCTTC
* *
950 CAAAATT-CTATTTTTAACCCCAACCTTC
1 CAAAATTACCATTTTTAACCCAAACCTTC
978 CAAAATTACCATTTT
1 CAAAATTACCATTTT
993 ACCCTCGGAT
Statistics
Matches: 80, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
28 21 0.26
29 25 0.31
30 30 0.38
31 4 0.05
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.40
Consensus pattern (29 bp):
CAAAATTACCATTTTTAACCCAAACCTTC
Found at i:992 original size:28 final size:28
Alignment explanation
Indices: 903--993 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 28
893 AAAATTTCAT
*
903 TTTTAACCCTAACCTTTCCAAAAATTA-CA
1 TTTTAACCCAAACC-TTCC-AAAATTACCA
** *
932 TTTT-ACTCCTAAATTTTCCAAAATT-CTA
1 TTTTAAC-CC-AAACCTTCCAAAATTACCA
*
960 TTTTTAACCCCAACCTTCCAAAATTACCA
1 -TTTTAACCCAAACCTTCCAAAATTACCA
989 TTTTA
1 TTTTA
994 CCCTCGGATG
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
28 26 0.54
29 18 0.38
30 4 0.08
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (28 bp):
TTTTAACCCAAACCTTCCAAAATTACCA
Found at i:1011 original size:29 final size:29
Alignment explanation
Indices: 979--1231 Score: 171
Period size: 29 Copynumber: 8.6 Consensus size: 29
969 CCAACCTTCC
* *
979 AAAATTACCATTTTACCCTCGGATGTTTA
1 AAAATTACCATTTTACCCTCGAATGTCTA
** **
1008 AAAATT-CCATTTTTAGCCCT-GAACCTCCC
1 AAAATTACCA-TTTTA-CCCTCGAATGTCTA
*
1037 AAAATTACCATTTTACCCCCGAATGTCTA
1 AAAATTACCATTTTACCCTCGAATGTCTA
* * * * * *
1066 AAAAAT-CCATTTTAACCTCTTATTTTCCA
1 AAAATTACCATTTTACCCTC-GAATGTCTA
*
1095 AAAATTACCATTTTATCCTCGAATGTCTA
1 AAAATTACCATTTTACCCTCGAATGTCTA
*
1124 AAAATT-CCATTTTTTAACCC-CGAACT-TTTCA
1 AAAATTACCA--TTTT-ACCCTCGAA-TGTCT-A
*
1155 AAAATTACCATTTTACCCCCGAATGTCTA
1 AAAATTACCATTTTACCCTCGAATGTCTA
* * * *
1184 AAAATT-CCGTTTTTTA-CTTCGAACTTTCCA
1 AAAATTACC--ATTTTACCCTCGAA-TGTCTA
1214 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
1232 CCAAGTGTCC
Statistics
Matches: 171, Mismatches: 34, Indels: 37
0.71 0.14 0.15
Matches are distributed among these distances:
28 22 0.13
29 78 0.46
30 55 0.32
31 13 0.08
32 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAATGTCTA
Found at i:1051 original size:58 final size:58
Alignment explanation
Indices: 892--1231 Score: 309
Period size: 58 Copynumber: 5.8 Consensus size: 58
882 TAAATTTTCC
* * *
892 AAAAATTTCATTTTTAACCCT-AACCTTTCCAAAAATTA-CATTTTACTCCT-AAAT-TTT
1 AAAAATTCCATTTTTAACCCTGAACC--TCCAAAAATTACCATTTTAC-CCTCGAATGTCT
* * * * *
949 CCAAAATTCTATTTTTAACCC-CAACCTTCC-AAAATTACCATTTTACCCTCGGATGTTT
1 -AAAAATTCCATTTTTAACCCTGAACC-TCCAAAAATTACCATTTTACCCTCGAATGTCT
* * *
1007 AAAAATTCCATTTTTAGCCCTGAACCTCCCAAAATTACCATTTTACCCCCGAATGTCT
1 AAAAATTCCATTTTTAACCCTGAACCTCCAAAAATTACCATTTTACCCTCGAATGTCT
* * *** *
1065 AAAAAATCCA-TTTTAACCTCTTATTTTCCAAAAATTACCATTTTATCCTCGAATGTCT
1 AAAAATTCCATTTTTAACC-CTGAACCTCCAAAAATTACCATTTTACCCTCGAATGTCT
* * * *
1123 AAAAATTCCATTTTTTAACCCCGAACTTTTCAAAAATTACCATTTTACCCCCGAATGTCT
1 AAAAATTCCA-TTTTTAACCCTGAAC-CTCCAAAAATTACCATTTTACCCTCGAATGTCT
* * * *
1183 AAAAATTCCGTTTTTTA-CTTCGAACTTTCCAAAAATTACCATTTTACCC
1 AAAAATTCCATTTTTAACCCT-GAAC-CTCCAAAAATTACCATTTTACCC
1232 CCAAGTGTCC
Statistics
Matches: 237, Mismatches: 34, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
56 10 0.04
57 41 0.17
58 104 0.44
59 35 0.15
60 47 0.20
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (58 bp):
AAAAATTCCATTTTTAACCCTGAACCTCCAAAAATTACCATTTTACCCTCGAATGTCT
Done.