Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006218.1 Kokia drynarioides strain JFW-HI SEQ_120789, 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: 83349
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1934 original size:2 final size:2
Alignment explanation
Indices: 1927--1959 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1917 ATAATGCAAT
1927 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1960 GTTTGATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2089 original size:2 final size:2
Alignment explanation
Indices: 2084--2109 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2074 CCCAAAAAAG
2084 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
2110 TAACAACGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3501 original size:2 final size:2
Alignment explanation
Indices: 3494--3525 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3484 GATTTCTTTA
*
3494 AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3526 TTTAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3853 original size:30 final size:30
Alignment explanation
Indices: 3819--3891 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
3809 TTGTGTACAT
* *
3819 AAACTTTAATTTGGTGCAATTATACACGTG
1 AAACTTTAATTTGGTGAAAATATACACGTG
* * * *
3849 AAACTCTAATTGTGGTTAAAATGTACACTTG
1 AAACTTTAATT-TGGTGAAAATATACACGTG
3880 AAACTTTAATTT
1 AAACTTTAATTT
3892 TGATTTAATC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (30 bp):
AAACTTTAATTTGGTGAAAATATACACGTG
Found at i:9985 original size:73 final size:73
Alignment explanation
Indices: 9897--10044 Score: 278
Period size: 73 Copynumber: 2.0 Consensus size: 73
9887 TAATTTTACT
9897 TTTATTTAATAAAAACTTTATAAATCTTTTAGAACTAAAAACATAATTTTTCATTATGGAAGCCA
1 TTTATTTAATAAAAACTTTATAAATCTTTTAGAACTAAAAACATAATTTTTCATTATGGAAGCCA
9962 GGGCCTGC
66 GGGCCTGC
* *
9970 TTTATTTAATTAAAACTTTATAAATCTTTTAGAACTAAAAACATAATTTTTCATTATGGAAGCCT
1 TTTATTTAATAAAAACTTTATAAATCTTTTAGAACTAAAAACATAATTTTTCATTATGGAAGCCA
10035 GGGCCTGC
66 GGGCCTGC
10043 TT
1 TT
10045 GCCTTTCCTT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (73 bp):
TTTATTTAATAAAAACTTTATAAATCTTTTAGAACTAAAAACATAATTTTTCATTATGGAAGCCA
GGGCCTGC
Found at i:11191 original size:29 final size:31
Alignment explanation
Indices: 11154--11213 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
11144 TTTAAATATG
*
11154 AAATATTAATTTT-TA-TATCATAAAAAAACT
1 AAATATTAATTTTAAATTA-CATAAAAAAACT
11184 AAAT-TTAATTTTAAATTACATAAAAAAACT
1 AAATATTAATTTTAAATTACATAAAAAAACT
11214 TTGATTTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 8 0.30
30 17 0.63
31 2 0.07
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (31 bp):
AAATATTAATTTTAAATTACATAAAAAAACT
Found at i:11497 original size:17 final size:18
Alignment explanation
Indices: 11475--11511 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
11465 TAACACGAGT
*
11475 TATTTAA-AAATTTTATA
1 TATTTAACAAATCTTATA
11492 TATTTAACAAATCTTATA
1 TATTTAACAAATCTTATA
11510 TA
1 TA
11512 ATAATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTTAACAAATCTTATA
Found at i:17797 original size:2 final size:2
Alignment explanation
Indices: 17790--17831 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
17780 TTACTGTGTA
17790 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
17832 TATGTACATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26046 original size:24 final size:24
Alignment explanation
Indices: 26003--26051 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
25993 CGGCTAACGG
*
26003 ATTCAAATTTAGTTATTTTA-GAA
1 ATTCAAATTTAGCTATTTTACGAA
26026 ATTCATAATTTCAGCTA-TTTACGAA
1 ATTCA-AATTT-AGCTATTTTACGAA
26051 A
1 A
26052 ATTTGATGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 5 0.23
24 9 0.41
25 8 0.36
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (24 bp):
ATTCAAATTTAGCTATTTTACGAA
Found at i:37506 original size:29 final size:30
Alignment explanation
Indices: 37465--37538 Score: 114
Period size: 29 Copynumber: 2.5 Consensus size: 30
37455 TTATAGGGAT
37465 TGGATCAAATTAATCCCTATATTATT-AAA
1 TGGATCAAATTAATCCCTATATTATTAAAA
*
37494 TGGATCAATTTAATCCCTATATTATTAAAA
1 TGGATCAAATTAATCCCTATATTATTAAAA
* *
37524 AGGATCAAATAAATC
1 TGGATCAAATTAATC
37539 TAAATTGTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (30 bp):
TGGATCAAATTAATCCCTATATTATTAAAA
Found at i:45636 original size:2 final size:2
Alignment explanation
Indices: 45619--45664 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
45609 TACTTTAACA
* *
45619 TC TC TT TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
45661 TC TC
1 TC TC
45665 GTCAATCACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:49783 original size:18 final size:18
Alignment explanation
Indices: 49760--49802 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
49750 AAATAATTTT
49760 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
49778 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
49796 TTAATTA
1 TTAATTA
49803 CAACTGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:59822 original size:26 final size:22
Alignment explanation
Indices: 59753--59809 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
59743 TAGAGTTAAC
59753 ATTTATTGTTTAAAATAATATT
1 ATTTATTGTTTAAAATAATATT
59775 ATTTATTGTTTAAAATAATATT
1 ATTTATTGTTTAAAATAATATT
59797 ATTTATTGTTTAA
1 ATTTATTGTTTAA
59810 TAGAATTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (22 bp):
ATTTATTGTTTAAAATAATATT
Found at i:60719 original size:77 final size:77
Alignment explanation
Indices: 60628--60776 Score: 289
Period size: 77 Copynumber: 1.9 Consensus size: 77
60618 TATTCATAAT
60628 TTCAAGTATCAAAATGAGAAAAACAAGTACTGAAACGAGAAAAAATATAATTTAGGAGTAAAATC
1 TTCAAGTATCAAAATGAGAAAAACAAGTACTGAAACGAGAAAAAATATAATTTAGGAGTAAAATC
60693 ATGATTTTATTC
66 ATGATTTTATTC
*
60705 TTCAAGTATCAAAATGAGGAAAACAAGTACTGAAACGAGAAAAAATATAATTTAGGAGTAAAATC
1 TTCAAGTATCAAAATGAGAAAAACAAGTACTGAAACGAGAAAAAATATAATTTAGGAGTAAAATC
60770 ATGATTT
66 ATGATTT
60777 AAGAATAAAA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (77 bp):
TTCAAGTATCAAAATGAGAAAAACAAGTACTGAAACGAGAAAAAATATAATTTAGGAGTAAAATC
ATGATTTTATTC
Found at i:63582 original size:29 final size:30
Alignment explanation
Indices: 63540--63597 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
63530 CTTGATCATA
*
63540 TTAGTCCCTCTACTATT-AAATGGATCAAT
1 TTAGTCCCTCTACTATTAAAATGAATCAAT
* *
63569 TTAGTCTCTGTACTATTAAAATGAATCAA
1 TTAGTCCCTCTACTATTAAAATGAATCAA
63598 ATAAGGCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.38
Consensus pattern (30 bp):
TTAGTCCCTCTACTATTAAAATGAATCAAT
Found at i:63809 original size:30 final size:30
Alignment explanation
Indices: 63775--63838 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
63765 TTGGACTTAT
** *
63775 TTGATTCTTTTTAATAGTACAGGGACTAAA
1 TTGATTCCATTTAATAATACAGGGACTAAA
* *
63805 TTGA-TCCATTTAATAATAGAGGGACTAAT
1 TTGATTCCATTTAATAATACAGGGACTAAA
63834 TTGAT
1 TTGAT
63839 CCAGTCACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.39
Consensus pattern (30 bp):
TTGATTCCATTTAATAATACAGGGACTAAA
Found at i:63827 original size:29 final size:29
Alignment explanation
Indices: 63784--63859 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
63774 TTTGATTCTT
*
63784 TTTAATAGTACAGGGACTAAATTGATCCA
1 TTTAATAATACAGGGACTAAATTGATCCA
* *
63813 TTTAATAATAGAGGGACTAATTTGATCCA
1 TTTAATAATACAGGGACTAAATTGATCCA
* *
63842 GTCACTATAATACAGGGA
1 TTTA--ATAATACAGGGA
63860 TCTCCCAGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 28 0.72
31 11 0.28
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (29 bp):
TTTAATAATACAGGGACTAAATTGATCCA
Found at i:75874 original size:3 final size:3
Alignment explanation
Indices: 75866--75895 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
75856 ACAAGTGTCT
75866 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
75896 AATAAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Done.