Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014095.1 Kokia drynarioides strain JFW-HI SEQ_129126, 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: 80830
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1962 original size:2 final size:2
Alignment explanation
Indices: 1955--1982 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1945 CAGTGATCCC
1955 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1983 TTTTTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:13648 original size:27 final size:27
Alignment explanation
Indices: 13610--13664 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
13600 TCGGAATATT
13610 ATGAAGTTTAATAGAATTCTGCAACTC
1 ATGAAGTTTAATAGAATTCTGCAACTC
13637 ATGAAGTTTAATAGAATTCTGCAACTC
1 ATGAAGTTTAATAGAATTCTGCAACTC
13664 A
1 A
13665 AGTTCTTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (27 bp):
ATGAAGTTTAATAGAATTCTGCAACTC
Found at i:37218 original size:22 final size:22
Alignment explanation
Indices: 37191--37233 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
37181 ATCTATACTC
* *
37191 TTTTTCTCCTAATAAATTATTA
1 TTTTTCTCCAAAAAAATTATTA
37213 TTTTTCTCCAAAAAAATTATT
1 TTTTTCTCCAAAAAAATTATT
37234 GTTACTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.14, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTTCTCCAAAAAAATTATTA
Found at i:37306 original size:25 final size:25
Alignment explanation
Indices: 37277--37368 Score: 96
Period size: 25 Copynumber: 3.6 Consensus size: 25
37267 AAAGGGAAGG
37277 AAAGGAAAAGATATAAAGATTAAGC
1 AAAGGAAAAGATATAAAGATTAAGC
* * * *
37302 AAAGGAAATGATAT-ATGTTTGGGAAGG
1 AAAGGAAAAGATATAAAGATT---AAGC
*
37329 AAAGGAAAAGATAGAAAGATTAAGC
1 AAAGGAAAAGATATAAAGATTAAGC
*
37354 AAAGGAAATGATATA
1 AAAGGAAAAGATATA
37369 TGTTTTTTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
24 4 0.08
25 29 0.56
27 15 0.29
28 4 0.08
ACGTcount: A:0.54, C:0.02, G:0.25, T:0.18
Consensus pattern (25 bp):
AAAGGAAAAGATATAAAGATTAAGC
Found at i:37348 original size:52 final size:52
Alignment explanation
Indices: 37270--37373 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
37260 TAATTGTAAA
*
37270 GGGAAGGAAAGGAAAAGATATAAAGATTAAGCAAAGGAAATGATATATGTTT
1 GGGAAGGAAAGGAAAAGATAGAAAGATTAAGCAAAGGAAATGATATATGTTT
37322 GGGAAGGAAAGGAAAAGATAGAAAGATTAAGCAAAGGAAATGATATATGTTT
1 GGGAAGGAAAGGAAAAGATAGAAAGATTAAGCAAAGGAAATGATATATGTTT
37374 TTTTTTTAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.50, C:0.02, G:0.28, T:0.20
Consensus pattern (52 bp):
GGGAAGGAAAGGAAAAGATAGAAAGATTAAGCAAAGGAAATGATATATGTTT
Found at i:44811 original size:30 final size:28
Alignment explanation
Indices: 44777--44840 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 28
44767 TCCTTTTGGA
* *
44777 TTTAAAATTTTAAAAATATTTAATAGATAT
1 TTTAAAATTTAAAAAATATTAAAT-GA-AT
*
44807 TTTAATATTTAAAAAATATTAAATGAAT
1 TTTAAAATTTAAAAAATATTAAATGAAT
44835 TTTAAA
1 TTTAAA
44841 TATAAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 7 0.23
29 2 0.07
30 21 0.70
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (28 bp):
TTTAAAATTTAAAAAATATTAAATGAAT
Found at i:44818 original size:29 final size:26
Alignment explanation
Indices: 44776--44853 Score: 77
Period size: 30 Copynumber: 2.8 Consensus size: 26
44766 ATCCTTTTGG
*
44776 ATTTAAAATTTTAAAAATATTTAATAGA
1 ATTTTAAA-TTTAAAAATATTTAAT-GA
*
44804 TATTTTAATATTTAAAAAATATTAAATGA
1 -ATTTTAA-ATTT-AAAAATATTTAATGA
*
44833 ATTTTAAATAT-AAAATATTTA
1 ATTTTAAATTTAAAAATATTTA
44854 TCAATTATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
25 9 0.21
27 3 0.07
28 7 0.16
29 11 0.26
30 13 0.30
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (26 bp):
ATTTTAAATTTAAAAATATTTAATGA
Found at i:44868 original size:20 final size:21
Alignment explanation
Indices: 44837--44888 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
44827 AAATGAATTT
* *
44837 TAAATATAAAATATTTATCAA
1 TAAATTTAAAATATTCATCAA
*
44858 T-TATTTAAAATATTCATCAA
1 TAAATTTAAAATATTCATCAA
44878 TAAATTTAAAA
1 TAAATTTAAAA
44889 ATAAAAATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAAAATATTCATCAA
Found at i:46055 original size:20 final size:20
Alignment explanation
Indices: 46030--46071 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
46020 GTTCCCGAAT
46030 CACCGGCACAAAGCCTGATA
1 CACCGGCACAAAGCCTGATA
* *
46050 CACCGGCATAAAGGCTGATA
1 CACCGGCACAAAGCCTGATA
46070 CA
1 CA
46072 TAGAATGCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.31, G:0.21, T:0.12
Consensus pattern (20 bp):
CACCGGCACAAAGCCTGATA
Found at i:47489 original size:3 final size:3
Alignment explanation
Indices: 47481--47511 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
47471 CAAGGCCTGT
*
47481 TCA TCA TCA TCA TCA CCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
47512 AATAGTCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
TCA
Found at i:56503 original size:22 final size:21
Alignment explanation
Indices: 56477--56520 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
56467 TTTTTAAAAA
*
56477 AATATTTATATTATATTATTTT
1 AATATTTATAATATATT-TTTT
*
56499 AATATTTTTAATATATTTTTT
1 AATATTTATAATATATTTTTT
56520 A
1 A
56521 TTTATTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
AATATTTATAATATATTTTTT
Found at i:57429 original size:17 final size:17
Alignment explanation
Indices: 57407--57440 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
57397 AAAAAAATTC
*
57407 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
57424 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
57441 TCATGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:57954 original size:29 final size:32
Alignment explanation
Indices: 57922--57981 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
57912 TGTTTCTATT
57922 ATATTAAAA-TTT-AA-AAAAAATATTTTTGA
1 ATATTAAAATTTTAAATAAAAAATATTTTTGA
57951 ATATTAAAATTTTGAAATAAAAAATATTTTT
1 ATATTAAAATTTT-AAATAAAAAATATTTTT
57982 AAAATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 9 0.33
30 3 0.11
32 2 0.07
33 13 0.48
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (32 bp):
ATATTAAAATTTTAAATAAAAAATATTTTTGA
Found at i:58660 original size:14 final size:14
Alignment explanation
Indices: 58641--58670 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
58631 CAGCTGGATT
58641 TGGAGCTGCTTCAC
1 TGGAGCTGCTTCAC
58655 TGGAGCTGCTTCAC
1 TGGAGCTGCTTCAC
58669 TG
1 TG
58671 ATCCAGACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.27, G:0.30, T:0.30
Consensus pattern (14 bp):
TGGAGCTGCTTCAC
Found at i:60566 original size:17 final size:17
Alignment explanation
Indices: 60534--60566 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
60524 CAAACATAAA
60534 AAATATTAAATAAATTC
1 AAATATTAAATAAATTC
60551 AAAT-TTAAATAGAATT
1 AAATATTAAATA-AATT
60567 AATTCCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
AAATATTAAATAAATTC
Found at i:63388 original size:25 final size:27
Alignment explanation
Indices: 63330--63385 Score: 89
Period size: 26 Copynumber: 2.1 Consensus size: 27
63320 TTCTGCTAAT
*
63330 ATTTTG-TTTCCTTTTCTTCTTCAAAA
1 ATTTTGCTTTCCTTTCCTTCTTCAAAA
63356 ATTTTGCTTT-CTTTCCTTCTTCAAAA
1 ATTTTGCTTTCCTTTCCTTCTTCAAAA
63382 ATTT
1 ATTT
63386 GCTGTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 25 0.89
27 3 0.11
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.57
Consensus pattern (27 bp):
ATTTTGCTTTCCTTTCCTTCTTCAAAA
Found at i:66352 original size:21 final size:21
Alignment explanation
Indices: 66328--66379 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
66318 CGTATTTTTT
66328 TTTTAATAATTTTATTATA-AA
1 TTTTAATAATTTT-TTATACAA
*
66349 TTTTGAT-ATTTTTTATACAA
1 TTTTAATAATTTTTTATACAA
66369 TATTTAA-AATT
1 T-TTTAATAATT
66380 ATCATAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 5 0.19
20 8 0.31
21 13 0.50
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTAATAATTTTTTATACAA
Found at i:73336 original size:5 final size:5
Alignment explanation
Indices: 73326--73352 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
73316 ACCCCCTCCT
73326 CCTTC CCTTC CCTTC CCTTC CCTTC CC
1 CCTTC CCTTC CCTTC CCTTC CCTTC CC
73353 AGCCTGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (5 bp):
CCTTC
Done.