Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012389.1 Kokia drynarioides strain JFW-HI SEQ_127393, 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: 7366
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--29 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
30 TCAAAATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:781 original size:6 final size:6
Alignment explanation
Indices: 727--849 Score: 71
Period size: 6 Copynumber: 21.2 Consensus size: 6
717 ACATTTTATT
* * ** *
727 ATTTAA ATTTAGA A--TAA TTTTAA ATATAA ATTTAA ACATAG A-TTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
** **
773 ATTTAA ATTCTAA A-GCAA ATTTAA ATTTAA AAATAA ATTTAA ATTTAA
1 ATTTAA ATT-TAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
821 A-ATAA ATTT-A ATCTTAA A-GTAA ATTTAA A
1 ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA A
850 ATGGGATTAG
Statistics
Matches: 86, Mismatches: 21, Indels: 20
0.68 0.17 0.16
Matches are distributed among these distances:
4 1 0.01
5 19 0.22
6 58 0.67
7 8 0.09
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (6 bp):
ATTTAA
Found at i:822 original size:17 final size:17
Alignment explanation
Indices: 745--849 Score: 104
Period size: 17 Copynumber: 6.0 Consensus size: 17
735 TTAGAATAAT
745 TTTAAATATAAATTTAAA
1 TTTAAA-ATAAATTTAAA
** * *
763 CATAGATTAAATTTAAA
1 TTTAAAATAAATTTAAA
**
780 TTCTAAAGCAAATTTAAA
1 TT-TAAAATAAATTTAAA
798 TTTAAAAATAAATTTAAA
1 TTT-AAAATAAATTTAAA
816 TTTAAAATAAATTT-AA
1 TTTAAAATAAATTTAAA
*
832 TCTTAAAGTAAATTTAAA
1 T-TTAAAATAAATTTAAA
850 ATGGGATTAG
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
16 3 0.04
17 34 0.48
18 34 0.48
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:1071 original size:18 final size:18
Alignment explanation
Indices: 1038--1073 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1028 AATTTCAAGA
**
1038 TTTTATTTTTCTATAATT
1 TTTTATTTTTAAATAATT
1056 TTTTATTTTTAAATAATT
1 TTTTATTTTTAAATAATT
1074 AAGTTTTTTT
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:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTATTTTTAAATAATT
Found at i:2100 original size:20 final size:20
Alignment explanation
Indices: 2087--2130 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2077 TTAATATATT
*
2087 TTTTAGAATTTTAAAAATTA
1 TTTTAAAATTTTAAAAATTA
*
2107 TTTTAAAATTTTGAAAATTA
1 TTTTAAAATTTTAAAAATTA
2127 TTTT
1 TTTT
2131 GAATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTTAAAATTTTAAAAATTA
Found at i:2138 original size:20 final size:20
Alignment explanation
Indices: 2093--2153 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2083 TATTTTTTAG
*
2093 AATTTTAAAAATTATTTTAA
1 AATTTTAAAAATTATTTTGA
*
2113 AATTTTGAAAATTATTTTGA
1 AATTTTAAAAATTATTTTGA
* **
2133 ATTTTTTTAAATTATTGTTGA
1 AATTTTAAAAATTATT-TTGA
2154 GAGATCAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 31 0.89
21 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (20 bp):
AATTTTAAAAATTATTTTGA
Found at i:3595 original size:29 final size:28
Alignment explanation
Indices: 3563--3625 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
3553 AAATGAGACT
3563 TTTTGGATACTCGGGGGCAAAAATGGTAA
1 TTTTGGATACTCGGGGG-AAAAATGGTAA
* ** *
3592 TTTTGGATTCTCTTGGGTAAAATGGTAA
1 TTTTGGATACTCGGGGGAAAAATGGTAA
3620 TTTTGG
1 TTTTGG
3626 GAAAATTTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.25, C:0.08, G:0.29, T:0.38
Consensus pattern (28 bp):
TTTTGGATACTCGGGGGAAAAATGGTAA
Found at i:3635 original size:28 final size:28
Alignment explanation
Indices: 3582--3636 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
3572 CTCGGGGGCA
***
3582 AAAATGGTAATTTTGGATTCTCTTGGGT
1 AAAATGGTAATTTTGGAAAATCTTGGGT
3610 AAAATGGTAATTTTGGGAAAAT-TTGGG
1 AAAATGGTAATTTT-GGAAAATCTTGGG
3637 GTTAACAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (28 bp):
AAAATGGTAATTTTGGAAAATCTTGGGT
Found at i:3713 original size:30 final size:30
Alignment explanation
Indices: 3677--3811 Score: 141
Period size: 30 Copynumber: 4.5 Consensus size: 30
3667 GTAAAGGGGT
* *
3677 AATTTT-GAGAGTTTCGAGGTCGAGAATGGA
1 AATTTTGGA-AGTTTCGAGGTCAAAAATGGA
* * *
3707 AATTTTGG-AGGTTCGGGGGTAAAAAATGGA
1 AATTTTGGAAGTTTC-GAGGTCAAAAATGGA
* *
3737 ATTTTTGGAAGTTTCAAGGTCAAAAATGGA
1 AATTTTGGAAGTTTCGAGGTCAAAAATGGA
* *
3767 ATTTTTGGAAGTTTCGAGGGT-AAAAATGAA
1 AATTTTGGAAGTTTCGA-GGTCAAAAATGGA
3797 AATTTTGGAAGTTTC
1 AATTTTGGAAGTTTC
3812 AGGGGTAAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
29 5 0.06
30 74 0.84
31 9 0.10
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (30 bp):
AATTTTGGAAGTTTCGAGGTCAAAAATGGA
Found at i:3757 original size:60 final size:60
Alignment explanation
Indices: 3677--3812 Score: 168
Period size: 60 Copynumber: 2.3 Consensus size: 60
3667 GTAAAGGGGT
* * * * *
3677 AATTTT-GAGAGTTTCGAGGTCGAGAATGGAAATTTTGG-AGGTTCGGGGGTAAAAAATGGA
1 AATTTTGGA-AGTTTCAAGGTCAAAAATGGAAATTTTGGAAGGTTCGAGGGT-AAAAATGAA
* * *
3737 ATTTTTGGAAGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGAA
1 AATTTTGGAAGTTTCAAGGTCAAAAATGGAAATTTTGGAAGGTTCGAGGGTAAAAATGAA
3797 AATTTTGGAAGTTTCA
1 AATTTTGGAAGTTTCA
3813 GGGGTAAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 53 0.82
61 12 0.18
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (60 bp):
AATTTTGGAAGTTTCAAGGTCAAAAATGGAAATTTTGGAAGGTTCGAGGGTAAAAATGAA
Found at i:3818 original size:30 final size:30
Alignment explanation
Indices: 3701--3859 Score: 166
Period size: 30 Copynumber: 5.4 Consensus size: 30
3691 CGAGGTCGAG
* * *
3701 AATGGAAATTTTGG-AGGTTCGGGGGTAAAA
1 AATGGAATTTTTGGAAGTTTCAGGGGT-AAA
*
3731 AATGGAATTTTTGGAAGTTTCA-AGGTCAAA
1 AATGGAATTTTTGGAAGTTTCAGGGGT-AAA
3761 AATGGAATTTTTGGAAGTTTC-GAGGGTAAA
1 AATGGAATTTTTGGAAGTTTCAG-GGGTAAA
* *
3791 AATGAAAATTTTGGAAGTTTCAGGGGTAAA
1 AATGGAATTTTTGGAAGTTTCAGGGGTAAA
** *
3821 AATTAAATTTTTGGGAG-TT-AGGGGTAAA
1 AATGGAATTTTTGGAAGTTTCAGGGGTAAA
*
3849 AATGGGATTTT
1 AATGGAATTTT
3860 CGAATAGTTT
Statistics
Matches: 111, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
28 17 0.15
29 2 0.02
30 83 0.75
31 9 0.08
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (30 bp):
AATGGAATTTTTGGAAGTTTCAGGGGTAAA
Found at i:3822 original size:60 final size:57
Alignment explanation
Indices: 3677--3852 Score: 167
Period size: 60 Copynumber: 3.0 Consensus size: 57
3667 GTAAAGGGGT
* * * * *
3677 AATTTT-GAGAGTTTCGAGGTCGAGAATGGAAATTTTGGAGGTTCGGGGGTAAAAAATGGA
1 AATTTTGGA-AGTTTCAAGGTCAAAAATGGAATTTTTGGA-GTTC-GGGGT-AAAAATGAA
*
3737 ATTTTTGGAAGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGAA
1 AATTTTGGAAGTTTCAAGGTCAAAAATGGAATTTTTGG-AG-TTCG-GGGTAAAAATGAA
* ** *
3797 AATTTTGGAAGTTTCAGGGGT-AAAAATTAAATTTTTGGGAGTTAGGGGTAAAAATG
1 AATTTTGGAAGTTTCA-AGGTCAAAAATGGAATTTTT-GGAGTTCGGGGTAAAAATG
3853 GGATTTTCGA
Statistics
Matches: 99, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
58 11 0.11
59 3 0.03
60 70 0.71
61 15 0.15
ACGTcount: A:0.35, C:0.04, G:0.30, T:0.32
Consensus pattern (57 bp):
AATTTTGGAAGTTTCAAGGTCAAAAATGGAATTTTTGGAGTTCGGGGTAAAAATGAA
Found at i:4426 original size:18 final size:19
Alignment explanation
Indices: 4389--4427 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
4379 TTTCTTTCTC
**
4389 CTTTCTTCAAAAAACCAAA
1 CTTTCTTCAAAAAAAAAAA
4408 CTTTCTT-AAAAAAAAAAA
1 CTTTCTTCAAAAAAAAAAA
4426 CT
1 CT
4428 CTCTCTCCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (19 bp):
CTTTCTTCAAAAAAAAAAA
Found at i:5682 original size:24 final size:22
Alignment explanation
Indices: 5644--5691 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
5634 AATTGGACTT
*
5644 AATTTAAATAGATTTAAACTTTA
1 AATTTAAATAAATTTAAA-TTTA
5667 AATTTATAATAAATTTAAATTTA
1 AATTTA-AATAAATTTAAATTTA
5690 AA
1 AA
5692 GTAAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTTAAATAAATTTAAATTTA
Found at i:5683 original size:17 final size:17
Alignment explanation
Indices: 5658--5737 Score: 115
Period size: 17 Copynumber: 4.6 Consensus size: 17
5648 TAAATAGATT
*
5658 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTAAAA
*
5676 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAA
*
5693 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
5710 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
5727 TAAATTTAAAT
1 TAAATTTAAAT
5738 CCTGTTGGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
17 51 0.93
18 4 0.07
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:5685 original size:6 final size:6
Alignment explanation
Indices: 5655--5737 Score: 68
Period size: 6 Copynumber: 14.3 Consensus size: 6
5645 ATTTAAATAG
*
5655 ATTTAA ACTTTAA ATTTATA A--TAA ATTTAA ATTTAA A-GTAA ATTTAA
1 ATTTAA A-TTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * *
5702 ACTTAA A-ATAA ATTTAA TTTTAA A-ATAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
5738 CCTGTTGGGT
Statistics
Matches: 61, Mismatches: 9, Indels: 14
0.73 0.11 0.17
Matches are distributed among these distances:
4 2 0.03
5 14 0.23
6 37 0.61
7 8 0.13
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (6 bp):
ATTTAA
Done.