Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004625.1 Kokia drynarioides strain JFW-HI SEQ_118140, 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: 74326
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3169 original size:27 final size:25
Alignment explanation
Indices: 3137--3186 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
3127 TAAATCAATT
3137 GAAAATATTAATTGATTTAATTTTTTC
1 GAAAAT-TTAATTGA-TTAATTTTTTC
* *
3164 GAAAATTTTATTTATTAATTTTT
1 GAAAATTTAATTGATTAATTTTT
3187 AGGTAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 6 0.29
27 6 0.29
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (25 bp):
GAAAATTTAATTGATTAATTTTTTC
Found at i:6289 original size:14 final size:14
Alignment explanation
Indices: 6272--6299 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6262 AAATTAATAC
6272 TAGATGATTAAAAG
1 TAGATGATTAAAAG
6286 TAGATGATTAAAAG
1 TAGATGATTAAAAG
6300 CAACTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (14 bp):
TAGATGATTAAAAG
Found at i:28988 original size:17 final size:17
Alignment explanation
Indices: 28968--29002 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28958 ATTTAATATG
28968 AAAATATAAAAAAAATA
1 AAAATATAAAAAAAATA
**
28985 AAAATATACTAAAAATA
1 AAAATATAAAAAAAATA
29002 A
1 A
29003 TATTTATTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAATATAAAAAAAATA
Found at i:37563 original size:7 final size:7
Alignment explanation
Indices: 37551--37577 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
37541 ACTGTTGGAG
37551 CCATTGT
1 CCATTGT
37558 CCATTGT
1 CCATTGT
37565 CCATTGT
1 CCATTGT
37572 CCATTG
1 CCATTG
37578 ACACAGATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.15, T:0.41
Consensus pattern (7 bp):
CCATTGT
Found at i:38248 original size:15 final size:14
Alignment explanation
Indices: 38226--38293 Score: 75
Period size: 14 Copynumber: 4.6 Consensus size: 14
38216 TTATACTACA
38226 AAATATTTATTATT
1 AAATATTTATTATT
38240 AATATATTTATATATAGT
1 AA-ATATTTAT-TAT--T
38258 AAATATTTATTATT
1 AAATATTTATTATT
*
38272 AAA-ATATTAATATT
1 AAATAT-TTATTATT
38286 AAATATTT
1 AAATATTT
38294 TTAATAATAT
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
13 2 0.04
14 18 0.38
15 10 0.21
16 6 0.13
17 8 0.17
18 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (14 bp):
AAATATTTATTATT
Found at i:38263 original size:32 final size:28
Alignment explanation
Indices: 38226--38303 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 28
38216 TTATACTACA
38226 AAATATTTATTATTAATATATTTATATATAGT
1 AAATATTTATTATTAATATA-TTA-ATAT--T
*
38258 AAATATTTATTATTAAAATATTAATATT
1 AAATATTTATTATTAATATATTAATATT
*
38286 AAATATTT-TTAATAATAT
1 AAATATTTATTATTAATAT
38304 GTGAAGAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 8 0.19
28 9 0.21
30 4 0.09
31 3 0.07
32 19 0.44
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (28 bp):
AAATATTTATTATTAATATATTAATATT
Found at i:38288 original size:28 final size:31
Alignment explanation
Indices: 38226--38293 Score: 97
Period size: 32 Copynumber: 2.3 Consensus size: 31
38216 TTATACTACA
*
38226 AAATATTTATTATTAATATATTTATATATAGT
1 AAATATTTATTATTAAAATATTTATATATA-T
38258 AAATATTTATTATTAAAATA-TTA-ATAT-T
1 AAATATTTATTATTAAAATATTTATATATAT
38286 AAATATTT
1 AAATATTT
38294 TTAATAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
28 9 0.26
30 4 0.11
31 3 0.09
32 19 0.54
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (31 bp):
AAATATTTATTATTAAAATATTTATATATAT
Found at i:38439 original size:25 final size:25
Alignment explanation
Indices: 38389--38439 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
38379 ATTTTAATAG
*
38389 ATTATATTAATTATATTAATACATT
1 ATTATATTAATTATATAAATACATT
38414 ATTATATT-ATTAAATATAAATA-ATT
1 ATTATATTAATT--ATATAAATACATT
38439 A
1 A
38440 AATATATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 3 0.13
25 12 0.52
26 8 0.35
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTATATTAATTATATAAATACATT
Found at i:47076 original size:21 final size:22
Alignment explanation
Indices: 47051--47092 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
47041 TTTTTTTAAT
47051 TTAAA-AATTAAAATTCTTTTG
1 TTAAACAATTAAAATTCTTTTG
* *
47072 TTAAACCATTAAAATTTTTTT
1 TTAAACAATTAAAATTCTTTT
47093 TTGTTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.50
Consensus pattern (22 bp):
TTAAACAATTAAAATTCTTTTG
Found at i:47507 original size:2 final size:2
Alignment explanation
Indices: 47500--47553 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
47490 TGTTCTTTTA
47500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
47542 AT A- AT AT TT AT A
1 AT AT AT AT AT AT A
47554 ACATATTTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62326 original size:209 final size:209
Alignment explanation
Indices: 61966--62793 Score: 1550
Period size: 209 Copynumber: 4.0 Consensus size: 209
61956 GAGCAAACAA
*
61966 ACCAGTGCTTTGAGCCTGGTGCTTAACTTAATTGGTTCATGCAATCATCTTAAGAGGACTGCATT
1 ACCAGTGCTTTGAGCCTGGTGCTTAACTTAATTGGTTCATGCAACCATCTTAAGAGGACTGCATT
*
62031 CAGTAAGGTCTAGTTTAAATCTTAGCATTTACTTATTTTCAAGCTGCAGTCTCTTTTCTACCAAA
66 CAGTAAGGTCTAGTTTAAATCTTAGCATTTACTTATTTTCAAGCTGCAGTCTCTTTCCTACCAAA
* *
62096 AAGTCAATGCTTCTAGCCAGGATGAATTGGTAAATGCTGAAAGAACCAATTCTCTAAAGTGTTTA
131 AAGTCAATGCTTCAAGCCAGGATGAATTGGTAAATGCTGAAAGAACCAATCCTCTAAAGTGTTTA
62161 TAAAAAGTCAATGC
196 TAAAAAGTCAATGC
*
62175 ACCAGTGCTTTGATCCTGGTGCTTAACTTAATTGGTTCATGCAACCATCTTAAGAGGACTGCATT
1 ACCAGTGCTTTGAGCCTGGTGCTTAACTTAATTGGTTCATGCAACCATCTTAAGAGGACTGCATT
62240 CAGTAAGGTCTAGTTTAAATCTTAGCATTTACTTATTTTCAAGCTGCAGTCTCTTTCCTACCAAA
66 CAGTAAGGTCTAGTTTAAATCTTAGCATTTACTTATTTTCAAGCTGCAGTCTCTTTCCTACCAAA
* *
62305 AAGTCAATGCTTCAAGCCAGGATGAATTGGTAAATTCTGAAAGAACCAATTCTCTAAAGTGTTTA
131 AAGTCAATGCTTCAAGCCAGGATGAATTGGTAAATGCTGAAAGAACCAATCCTCTAAAGTGTTTA
62370 TAAAAAGTCAATGC
196 TAAAAAGTCAATGC
62384 ACCAGTGCTTTGAGCCTGGTGCTTAACTTAATTGGTTCATGCAACCATCTTAAGAGGACTGCATT
1 ACCAGTGCTTTGAGCCTGGTGCTTAACTTAATTGGTTCATGCAACCATCTTAAGAGGACTGCATT
62449 CAGTAAGGTCTAGTTTAAATCTTAGCATTTACTTATTTTCAAGCTGCAGTCTCTTTCCTACCAAA
66 CAGTAAGGTCTAGTTTAAATCTTAGCATTTACTTATTTTCAAGCTGCAGTCTCTTTCCTACCAAA
62514 AAGTCAATGCTTCAAGCCAGGATGAATTGGTAAATGCTGAAAGAACCAATCCTCTAAAGTGTTTA
131 AAGTCAATGCTTCAAGCCAGGATGAATTGGTAAATGCTGAAAGAACCAATCCTCTAAAGTGTTTA
62579 TAAAAAGTCAATGC
196 TAAAAAGTCAATGC
*
62593 ACCAGTGTTTTGAGCCTGGTGCTTAACTTAATTGGTTCATGCAACCATCTTACA-AGGACTGCAT
1 ACCAGTGCTTTGAGCCTGGTGCTTAACTTAATTGGTTCATGCAACCATCTTA-AGAGGACTGCAT
62657 TCAGTAAGGTCTAGTTTAAATCTTAGCATTTACTTATTTTCAAGCTGCAGTCTCTTTCCTACCAA
65 TCAGTAAGGTCTAGTTTAAATCTTAGCATTTACTTATTTTCAAGCTGCAGTCTCTTTCCTACCAA
*
62722 AAAGTCAATGCTTCAAGCCAGGATGAATTGGTAAATGCTGAAAGAACCAATCCTCTGAAGTGTTT
130 AAAGTCAATGCTTCAAGCCAGGATGAATTGGTAAATGCTGAAAGAACCAATCCTCTAAAGTGTTT
*
62787 AGAAAAA
195 ATAAAAA
62794 ACTTCTTACA
Statistics
Matches: 607, Mismatches: 11, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
209 606 1.00
210 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (209 bp):
ACCAGTGCTTTGAGCCTGGTGCTTAACTTAATTGGTTCATGCAACCATCTTAAGAGGACTGCATT
CAGTAAGGTCTAGTTTAAATCTTAGCATTTACTTATTTTCAAGCTGCAGTCTCTTTCCTACCAAA
AAGTCAATGCTTCAAGCCAGGATGAATTGGTAAATGCTGAAAGAACCAATCCTCTAAAGTGTTTA
TAAAAAGTCAATGC
Found at i:68292 original size:8 final size:8
Alignment explanation
Indices: 68279--68303 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
68269 ATTAGTAGAG
68279 AACAAGAA
1 AACAAGAA
68287 AACAAGAA
1 AACAAGAA
68295 AACAAGAA
1 AACAAGAA
68303 A
1 A
68304 TTAGTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (8 bp):
AACAAGAA
Found at i:68295 original size:26 final size:27
Alignment explanation
Indices: 68232--68295 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
68222 GGGAGAACAG
68232 AACAAGAAATTAGTAGAGAACTTACTAAA
1 AACAAGAAATTAGTAGAGAAC-TAC-AAA
*
68261 AAAAAGAAATTAGTAGAGAAC-A-AGAA
1 AACAAGAAATTAGTAGAGAACTACA-AA
68287 AACAAGAAA
1 AACAAGAAA
68296 ACAAGAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 1 0.03
26 10 0.31
27 1 0.03
29 20 0.62
ACGTcount: A:0.62, C:0.08, G:0.16, T:0.14
Consensus pattern (27 bp):
AACAAGAAATTAGTAGAGAACTACAAA
Found at i:69756 original size:16 final size:15
Alignment explanation
Indices: 69722--69764 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
69712 TAATAATTAT
*
69722 AATAA-TTAGAAACAA
1 AATAATTTA-AAATAA
69737 AATAACTTTAAAATAA
1 AATAA-TTTAAAATAA
69753 AATAATTTAAAA
1 AATAATTTAAAA
69765 ACAAAGAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 12 0.48
16 10 0.40
17 3 0.12
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (15 bp):
AATAATTTAAAATAA
Found at i:69765 original size:16 final size:16
Alignment explanation
Indices: 69722--69769 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
69712 TAATAATTAT
*
69722 AATAA-TTAGAAACAA
1 AATAATTTAAAAACAA
*
69737 AATAACTTT-AAAATAA
1 AATAA-TTTAAAAACAA
69753 AATAATTTAAAAACAA
1 AATAATTTAAAAACAA
69769 A
1 A
69770 GAACAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 8 0.30
16 17 0.63
17 2 0.07
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (16 bp):
AATAATTTAAAAACAA
Found at i:69979 original size:154 final size:149
Alignment explanation
Indices: 69805--70218 Score: 506
Period size: 141 Copynumber: 2.8 Consensus size: 149
69795 AAAACACATA
* *
69805 AACATTAAACTAAACAAATAATTTGTAATAATTACTAACAAAATAACTTTAAATTAAATTAAAAA
1 AACATTAAACTAAACAAATAATTTATAATAATTAATAACAAAATAACTTTAAATTAAATTAAAAA
*
69870 TAACAAAACAATTTAACTTTCTTTTAACTTTCTTCCCTTTAATCTACTCTACTAAACAAATTTTT
66 -AACAAAA-AA-TTACCTTTCTTTTAACTTTCTTCCCTTTAATCTACTCTACTAAACAAA--TTT
69935 TTTTTATAAAAAATCACATAAACC
126 TTTTTATAAAAAATCACATAAACC
* *
69959 AACATTAAATTAAACAAATAATTTATAATAATTAATAAAAAAATAACTTTAAATTAAATT----A
1 AACATTAAACTAAACAAATAATTTATAATAATTAATAACAAAATAACTTTAAATTAAATTAAAAA
** * * * *
70020 AA-AAAAAATT-CCTTT-TTTTGGCTTTCTTCCCTTTAATATATTATAC-AATCAAATTTTTTTT
66 AACAAAAAATTACCTTTCTTTTAACTTTCTTCCCTTTAATCTACTCTACTAAACAAATTTTTTTT
*
70081 ATTAAAAATCACATAAACC
131 ATAAAAAATCACATAAACC
* * * * * *
70100 GACATTAAACTAAACAAA-ACATTTATAATTATTATTAACTATATAACTTTAAATTAAACTAAAA
1 AACATTAAACTAAACAAATA-ATTTATAATAATTAATAACAAAATAACTTTAAATTAAATTAAAA
* *
70164 ACAACAAAAAAATTACCTTTCTTTTAATTTTCTT-TCTTTAATCTACTCTACTAAA
65 A-AAC-AAAAAATTACCTTTCTTTTAACTTTCTTCCCTTTAATCTACTCTACTAAA
70219 GAAAAAAATT
Statistics
Matches: 221, Mismatches: 28, Indels: 26
0.80 0.10 0.09
Matches are distributed among these distances:
140 1 0.00
141 76 0.34
143 6 0.03
144 26 0.12
145 5 0.02
146 4 0.02
147 2 0.01
148 12 0.05
149 20 0.09
150 13 0.06
154 56 0.25
ACGTcount: A:0.47, C:0.14, G:0.01, T:0.38
Consensus pattern (149 bp):
AACATTAAACTAAACAAATAATTTATAATAATTAATAACAAAATAACTTTAAATTAAATTAAAAA
AACAAAAAATTACCTTTCTTTTAACTTTCTTCCCTTTAATCTACTCTACTAAACAAATTTTTTTT
ATAAAAAATCACATAAACC
Done.