Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014561.1 Kokia drynarioides strain JFW-HI SEQ_129600, 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: 265799
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 365 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:218461 original size:18 final size:18
Alignment explanation
Indices: 218438--218473 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
218428 TTTCTTAAGT
218438 AAAGCAAATCTTTTTCTA
1 AAAGCAAATCTTTTTCTA
* *
218456 AAAGCAATTGTTTTTCTA
1 AAAGCAAATCTTTTTCTA
218474 GAAGTAAGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (18 bp):
AAAGCAAATCTTTTTCTA
Found at i:219250 original size:4 final size:4
Alignment explanation
Indices: 219241--219265 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
219231 TAATAAGAAA
219241 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
219266 TTGTGTTGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:222870 original size:43 final size:43
Alignment explanation
Indices: 222794--222900 Score: 117
Period size: 43 Copynumber: 2.5 Consensus size: 43
222784 AACACTATTC
* * ** * *
222794 CCTAAAATTGAAAGTATGAGATTGATTGTGTGGAACATTG-TT
1 CCTAATATTGAAAGTATGTGAACGAATGAGTGGAACATTGTTT
*
222836 CTCTATTATTGAAAGTATGTGAACGAATGAGTGGAACATTGTTT
1 C-CTAATATTGAAAGTATGTGAACGAATGAGTGGAACATTGTTT
**
222880 CCTAATATTGATGGTATGTGA
1 CCTAATATTGAAAGTATGTGA
222901 TTGATTGAGA
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
42 1 0.02
43 49 0.92
44 3 0.06
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.36
Consensus pattern (43 bp):
CCTAATATTGAAAGTATGTGAACGAATGAGTGGAACATTGTTT
Found at i:223127 original size:28 final size:28
Alignment explanation
Indices: 223095--223190 Score: 115
Period size: 27 Copynumber: 3.4 Consensus size: 28
223085 TACCAAGGGG
223095 ATTGGCGATCTCTATCGCATTATTTGTT
1 ATTGGCGATCTCTATCGCATTATTTGTT
* *
223123 ATTGGCGATCTTTATCGCATTA-TTGAT
1 ATTGGCGATCTCTATCGCATTATTTGTT
**
223150 ATTGGCGATCTCTATAACATT-TTTCGTT
1 ATTGGCGATCTCTATCGCATTATTT-GTT
223178 ATTTGGCAGATCT
1 A-TTGGC-GATCT
223191 TCTGTATTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
27 24 0.41
28 24 0.41
29 5 0.09
30 5 0.09
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.45
Consensus pattern (28 bp):
ATTGGCGATCTCTATCGCATTATTTGTT
Found at i:223170 original size:27 final size:28
Alignment explanation
Indices: 223095--223164 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
223085 TACCAAGGGG
*
223095 ATTGGCGATCTCTATCGCATTATTTGTT
1 ATTGGCGATCTCTATCGCATTATTTGAT
*
223123 ATTGGCGATCTTTATCGCATTA-TTGAT
1 ATTGGCGATCTCTATCGCATTATTTGAT
223150 ATTGGCGATCTCTAT
1 ATTGGCGATCTCTAT
223165 AACATTTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 18 0.46
28 21 0.54
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.44
Consensus pattern (28 bp):
ATTGGCGATCTCTATCGCATTATTTGAT
Found at i:223742 original size:18 final size:20
Alignment explanation
Indices: 223699--223743 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
223689 TTGGAAGGAA
223699 AGGTGC-AGTGGTAGAGTGT
1 AGGTGCAAGTGGTAGAGTGT
223718 -GGTGCAAGT-GTAGA-TGT
1 AGGTGCAAGTGGTAGAGTGT
223735 AGGTGCAAG
1 AGGTGCAAG
223744 AGCAAATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 18 0.75
19 3 0.12
ACGTcount: A:0.24, C:0.07, G:0.44, T:0.24
Consensus pattern (20 bp):
AGGTGCAAGTGGTAGAGTGT
Found at i:228481 original size:30 final size:30
Alignment explanation
Indices: 228444--228530 Score: 138
Period size: 30 Copynumber: 2.9 Consensus size: 30
228434 TAGAACGGGA
*
228444 AACAGCCACAAAGGCTCCCATGTAACAGTG
1 AACAGCCACAAAGGCTCACATGTAACAGTG
*
228474 AATAGCCACAAAGGCTCACATGTAACAGTG
1 AACAGCCACAAAGGCTCACATGTAACAGTG
* *
228504 AACAACCACAAATGCTCACATGTAACA
1 AACAGCCACAAAGGCTCACATGTAACA
228531 ATGGAAAGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.41, C:0.28, G:0.16, T:0.15
Consensus pattern (30 bp):
AACAGCCACAAAGGCTCACATGTAACAGTG
Found at i:248466 original size:19 final size:19
Alignment explanation
Indices: 248439--248538 Score: 137
Period size: 19 Copynumber: 5.3 Consensus size: 19
248429 CAGTACAGTC
* *
248439 TATTACTCTTATGAGCCAG
1 TATTGCTCTTACGAGCCAG
*
248458 TATTGCTCTTGCGAGCCAG
1 TATTGCTCTTACGAGCCAG
* * *
248477 TATTGTTCTTATGAGCCAA
1 TATTGCTCTTACGAGCCAG
*
248496 TATTGCTCTTACGAGCTAG
1 TATTGCTCTTACGAGCCAG
248515 TATTGCTCTTACGAGCCAG
1 TATTGCTCTTACGAGCCAG
248534 TATTG
1 TATTG
248539 GTCATTTCTT
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 69 1.00
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (19 bp):
TATTGCTCTTACGAGCCAG
Found at i:258271 original size:22 final size:22
Alignment explanation
Indices: 258245--258287 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
258235 CTTTTGTCGA
258245 CGCATTTGGATCTCCTTATTGG
1 CGCATTTGGATCTCCTTATTGG
258267 CGCATTTGGATCTCCTTATTG
1 CGCATTTGGATCTCCTTATTG
258288 AAGCAACTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.42
Consensus pattern (22 bp):
CGCATTTGGATCTCCTTATTGG
Found at i:260300 original size:17 final size:16
Alignment explanation
Indices: 260266--260305 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
260256 CTTTAAGGAC
260266 AAGAAAAGCAAAAAGG
1 AAGAAAAGCAAAAAGG
260282 AAGAAAAG-AACAGAAGG
1 AAGAAAAGCAA-A-AAGG
260299 AAGAAAA
1 AAGAAAA
260306 AGCACCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 9 0.41
17 11 0.50
ACGTcount: A:0.70, C:0.05, G:0.25, T:0.00
Consensus pattern (16 bp):
AAGAAAAGCAAAAAGG
Found at i:260474 original size:17 final size:17
Alignment explanation
Indices: 260454--260490 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
260444 TTACAATTTA
*
260454 ATTGTCACTGCATTTGC
1 ATTGTCACTGCATTTCC
*
260471 ATTGTCATTGCATTTCC
1 ATTGTCACTGCATTTCC
260488 ATT
1 ATT
260491 TGTTATTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.46
Consensus pattern (17 bp):
ATTGTCACTGCATTTCC
Found at i:261992 original size:40 final size:39
Alignment explanation
Indices: 261937--262070 Score: 153
Period size: 40 Copynumber: 3.4 Consensus size: 39
261927 AGTTATCTTG
*
261937 GATAGAATTCAAGCTTCAGCTTAGTAGGCTATGAGCCGAT
1 GATAGAATTCAAGCTTC-GCTTAGCAGGCTATGAGCCGAT
* * *
261977 GATAGAATTCAAGCTTTGGCTTAGCAGGCTATGAGCTGGT
1 GATAGAATTCAAGC-TTCGCTTAGCAGGCTATGAGCCGAT
* * * *
262017 GATAAAATTCAAGCTTCGACTTAGCAGACTACGAGTC-AGT
1 GATAGAATTCAAGCTTCG-CTTAGCAGGCTATGAGCCGA-T
262057 GATAGAATTCAAGC
1 GATAGAATTCAAGC
262071 CAAGCTATGG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
39 3 0.04
40 74 0.94
41 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (39 bp):
GATAGAATTCAAGCTTCGCTTAGCAGGCTATGAGCCGAT
Found at i:264748 original size:28 final size:28
Alignment explanation
Indices: 264689--264748 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
264679 AAACCCAGAT
**
264689 CAAAATAATTCTCTATTGAGCAAGAGTT
1 CAAAATAATTCTCTATTGAGCAAGAGAC
* *
264717 CAAAATATTTCTCT-TATGAGCCAGAGAC
1 CAAAATAATTCTCTAT-TGAGCAAGAGAC
264745 CAAA
1 CAAA
264749 TTATCGCTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.28
Consensus pattern (28 bp):
CAAAATAATTCTCTATTGAGCAAGAGAC
Found at i:264786 original size:28 final size:28
Alignment explanation
Indices: 264753--264842 Score: 135
Period size: 28 Copynumber: 3.2 Consensus size: 28
264743 ACCAAATTAT
*
264753 CGCTCTTTCGAGCTAGAATACAGAACAA
1 CGCTCTTTCGAGCTAGAATACAGAATAA
* * *
264781 CACTCTTTCGAGCCAGAATACAAAATAA
1 CGCTCTTTCGAGCTAGAATACAGAATAA
*
264809 CGCTCTTTCGATCTAGAATACAGAATAA
1 CGCTCTTTCGAGCTAGAATACAGAATAA
264837 CGCTCT
1 CGCTCT
264843 CTTGAGCCTT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (28 bp):
CGCTCTTTCGAGCTAGAATACAGAATAA
Done.