Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011278.1 Kokia drynarioides strain JFW-HI SEQ_126257, 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: 18274
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:2159 original size:31 final size:29
Alignment explanation
Indices: 2124--2230 Score: 106
Period size: 31 Copynumber: 3.5 Consensus size: 29
2114 TTGGAAGTTC
2124 TAATTAAAATTTTTAAAACTTTTAGAAGGCG
1 TAATTAAAATTTTTAAAA-TTTT-GAAGGCG
* * *
2155 TAATTAGAATTTCTAATAAATTTGAAGAGCG
1 TAATTAAAATTTTTAA-AATTTTGAAG-GCG
* *
2186 TAATTAAAAGTTTTCAAAAATTTTGAAGGCA
1 TAATTAAAA-TTTT-TAAAATTTTGAAGGCG
*
2217 TAATGAAAATTTTT
1 TAATTAAAATTTTT
2231 TAGATTTTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
30 8 0.13
31 38 0.61
32 14 0.23
33 2 0.03
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (29 bp):
TAATTAAAATTTTTAAAATTTTGAAGGCG
Found at i:4078 original size:6 final size:6
Alignment explanation
Indices: 4067--4162 Score: 78
Period size: 6 Copynumber: 16.7 Consensus size: 6
4057 GGCCCAATAG
* * *
4067 AATTTA AATTT- ATTTTAA AATTT- AATTT- ATTTTA AGTTTA AATTT-
1 AATTTA AATTTA AATTT-A AATTTA AATTTA AATTTA AATTTA AATTTA
* * *
4112 ACTTAA AATTTA AATTT- -ATTATA AATTTA AGTTTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATT-TA AATTTA AATTTA AATTTA AATTTA
4159 AATT
1 AATT
4163 AATGTTCAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
4 3 0.04
5 17 0.24
6 45 0.62
7 7 0.10
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:4095 original size:17 final size:17
Alignment explanation
Indices: 4067--4162 Score: 113
Period size: 17 Copynumber: 5.6 Consensus size: 17
4057 GGCCCAATAG
4067 AATTTAAATTTATTTTAA
1 AATTTAAATTTATTTT-A
4085 AATTT-AATTTATTTTA
1 AATTTAAATTTATTTTA
* * *
4101 AGTTTAAATTTACTTAA
1 AATTTAAATTTATTTTA
*
4118 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
* *
4135 AATTTAAGTTTAAATTTA
1 AATTTAAATTT-ATTTTA
4153 AATTTAAATT
1 AATTTAAATT
4163 AATGTTCAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
16 5 0.08
17 42 0.65
18 18 0.28
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:5916 original size:29 final size:29
Alignment explanation
Indices: 5868--6093 Score: 169
Period size: 29 Copynumber: 7.7 Consensus size: 29
5858 AGGAGCTTCT
*
5868 AAAAATTCCATTTTTGACCCCAAAACTTTC
1 AAAAATTACATTTTT-ACCCCAAAACTTTC
* *
5898 AAAAATTACATTTTTACCCTC-GAACTTCC
1 AAAAATTACATTTTTACCC-CAAAACTTTC
5927 AAAAATT-CTATTTTTGACCCCAAAACTTTC
1 AAAAATTAC-ATTTTT-ACCCCAAAACTTTC
* ** *
5957 AAAAATTATCA-TTTTGCCCCCGAA-TGTCC
1 AAAAATTA-CATTTTTACCCCAAAACT-TTC
* *
5986 AAAAATTCCATTTTGACCCCAAAACTTTC
1 AAAAATTACATTTTTACCCCAAAACTTTC
* *
6015 AAAAATTACCATTTTT-CCCTC-GAA-TGTCC
1 AAAAATTA-CATTTTTACCC-CAAAACT-TTC
* * **
6044 AAAAATTCCATTTTTACCTCGTAACTTTC
1 AAAAATTACATTTTTACCCCAAAACTTTC
**
6073 AAAAATTACCCTTTTACCCCA
1 AAAAATTACATTTTTACCCCA
6094 GGATGTCCAA
Statistics
Matches: 153, Mismatches: 28, Indels: 31
0.72 0.13 0.15
Matches are distributed among these distances:
28 13 0.08
29 93 0.61
30 45 0.29
31 1 0.01
32 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAATTACATTTTTACCCCAAAACTTTC
Found at i:6028 original size:58 final size:59
Alignment explanation
Indices: 5868--6108 Score: 328
Period size: 58 Copynumber: 4.1 Consensus size: 59
5858 AGGAGCTTCT
*
5868 AAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTA-CATTTTTACCCTCGAACT-TCC
1 AAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTACCA-TTTTACCCCCGAA-TGTCC
* * *
5927 AAAAATTCTATTTTTGACCCCAAAACTTTCAAAAATTATCATTTTGCCCCCGAATGTCC
1 AAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTACCATTTTACCCCCGAATGTCC
* *
5986 AAAAATTCCA-TTTTGACCCCAAAACTTTCAAAAATTACCATTTTTCCCTCGAATGTCC
1 AAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTACCATTTTACCCCCGAATGTCC
* ** * * *
6044 AAAAATTCCATTTTT-ACCTCGTAACTTTCAAAAATTACCCTTTTACCCCAGGATGTCC
1 AAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTACCATTTTACCCCCGAATGTCC
6102 AAAAATT
1 AAAAATT
6109 TCGTTTTTTT
Statistics
Matches: 164, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
58 98 0.60
59 64 0.39
60 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (59 bp):
AAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTACCATTTTACCCCCGAATGTCC
Found at i:6146 original size:117 final size:117
Alignment explanation
Indices: 5868--6108 Score: 353
Period size: 117 Copynumber: 2.1 Consensus size: 117
5858 AGGAGCTTCT
5868 AAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTA-CATTTTTACCCTCGAACT-TCCAAAA
1 AAAAATTCCA-TTTTGACCCCAAAACTTTCAAAAATTACCATTTTT-CCCTCGAA-TGTCCAAAA
* * * *
5931 ATTCTATTTTTGACCCCAAAACTTTCAAAAATTATCATTTTGCCCCCGAATGTCC
63 ATTCCATTTTTGACCCCAAAACTTTCAAAAATTACCATTTTACCCCAGAATGTCC
5986 AAAAATTCCATTTTGACCCCAAAACTTTCAAAAATTACCATTTTTCCCTCGAATGTCCAAAAATT
1 AAAAATTCCATTTTGACCCCAAAACTTTCAAAAATTACCATTTTTCCCTCGAATGTCCAAAAATT
* ** * *
6051 CCATTTTT-ACCTCGTAACTTTCAAAAATTACCCTTTTACCCCAGGATGTCC
66 CCATTTTTGACCCCAAAACTTTCAAAAATTACCATTTTACCCCAGAATGTCC
6102 AAAAATT
1 AAAAATT
6109 TCGTTTTTTT
Statistics
Matches: 112, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
116 43 0.38
117 52 0.46
118 17 0.15
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (117 bp):
AAAAATTCCATTTTGACCCCAAAACTTTCAAAAATTACCATTTTTCCCTCGAATGTCCAAAAATT
CCATTTTTGACCCCAAAACTTTCAAAAATTACCATTTTACCCCAGAATGTCC
Found at i:6148 original size:59 final size:58
Alignment explanation
Indices: 6018--6187 Score: 170
Period size: 58 Copynumber: 2.9 Consensus size: 58
6008 AACTTTCAAA
* * * * * *
6018 AATTACCATTTTTCCCTCGAATGTCCAAAAATTCC-ATTTTTACCTCGTA-ACTTTC-AAA
1 AATTACCATTTTACCCTCGGATGTCCAAAACTTCCTTTTTTTA--TC-TAGATTTTCTAAG
* * *
6076 AATTACCCTTTTACCC-CAGGATGTCCAAAAATTTCGTTTTTTTATCCT-GATTTTCTAAG
1 AATTACCATTTTACCCTC-GGATGTCC-AAAACTTCCTTTTTTTAT-CTAGATTTTCTAAG
6135 AATTACCATTTTACCCTCGGATGTCCAAAACTTCCTTTTTTTATCTAGATTTT
1 AATTACCATTTTACCCTCGGATGTCCAAAACTTCCTTTTTTTATCTAGATTTT
6188 TTCTAAAAAT
Statistics
Matches: 93, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
57 3 0.03
58 50 0.54
59 33 0.35
60 7 0.08
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.42
Consensus pattern (58 bp):
AATTACCATTTTACCCTCGGATGTCCAAAACTTCCTTTTTTTATCTAGATTTTCTAAG
Found at i:6578 original size:96 final size:96
Alignment explanation
Indices: 6472--6656 Score: 241
Period size: 96 Copynumber: 1.9 Consensus size: 96
6462 ATAACTTTAA
* * *
6472 AATCGAGGCAATATTATT-TTAT-TTCGAGTT-TCGAAAATTTGCGCCTTAACTTATTAGGCATA
1 AATCGAGGCAATATT-TTCTTATCTTC-AATTCT-GAAAATTTGCGCCTTAACTTACTAGGCACA
**
6534 ATTTTTCTTCAAATCAAAATAATCGAATACCCTT
63 ACCTTTCTTCAAATCAAAATAATCGAATACCCTT
* **
6568 AATCGAGGCAATGTTTTCTTATCTTCAATTCTGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
1 AATCGAGGCAATATTTTCTTATCTTCAATTCTGAAAATTTGCGCCTTAACTTACTAGGCACAACC
*
6633 TTTCTTCAAATCAAGATAATCGAA
66 TTTCTTCAAATCAAAATAATCGAA
6657 CATCCTTTCC
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
95 2 0.03
96 71 0.92
97 4 0.05
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATATTTTCTTATCTTCAATTCTGAAAATTTGCGCCTTAACTTACTAGGCACAACC
TTTCTTCAAATCAAAATAATCGAATACCCTT
Done.