Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006900.1 Kokia drynarioides strain JFW-HI SEQ_121501, 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: 70110
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 70 characters in sequence are not A, C, G, or T
Found at i:2688 original size:18 final size:18
Alignment explanation
Indices: 2647--2690 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2637 CAGCAAGTGA
* **
2647 ATTTAAACTTAAAAAATT
1 ATTTAAAATTAAAAAAAC
*
2665 AATTAAAATTAAAAAAAC
1 ATTTAAAATTAAAAAAAC
2683 ATTTAAAA
1 ATTTAAAA
2691 AATTGTCGGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTTAAAATTAAAAAAAC
Found at i:4633 original size:67 final size:67
Alignment explanation
Indices: 4554--4688 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
4544 CATTAGACAA
*
4554 TGGGACCATTTCTAATAGATTAAAAGATTGAGGGACAGGGCTTGAAATTGGGGACCTCTTTTTAA
1 TGGGACCATTTCTAATAGATTAAAAGACTGAGGGACAGGGCTTGAAATTGGGGACCTCTTTTTAA
4619 TT
66 TT
*
4621 TGGGACCATTTCTAATGGATTAAAAGACTGAGGGACAGGGCTTGAAATTGGGGACCTCTTTTTAA
1 TGGGACCATTTCTAATAGATTAAAAGACTGAGGGACAGGGCTTGAAATTGGGGACCTCTTTTTAA
4686 TT
66 TT
4688 T
1 T
4689 TATCAATTCA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.33
Consensus pattern (67 bp):
TGGGACCATTTCTAATAGATTAAAAGACTGAGGGACAGGGCTTGAAATTGGGGACCTCTTTTTAA
TT
Found at i:8798 original size:28 final size:30
Alignment explanation
Indices: 8767--8822 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 30
8757 TCTAAAAAAG
*
8767 TAAAAAAAA-AAAAATTAA-ATTAAATTCC
1 TAAAAAAAATAAAAATAAATATTAAATTCC
*
8795 TAAAAAAAATAAACATAAATATTAAATT
1 TAAAAAAAATAAAAATAAATATTAAATT
8823 TCAAATTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.38
29 7 0.29
30 8 0.33
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (30 bp):
TAAAAAAAATAAAAATAAATATTAAATTCC
Found at i:13325 original size:60 final size:59
Alignment explanation
Indices: 13229--13488 Score: 208
Period size: 61 Copynumber: 4.3 Consensus size: 59
13219 ATATATATAT
* * *
13229 AATTTTTTTGTGTTGGCCATACAATGGCCGACACCCCTATTTATCTGA-TAAAAAAAATTGC
1 AATTTTTTTGTGTTGGCCATGCAATAGCCGACACCCCT-TTT-T-TGAGAAAAAAAAATTGC
* * * * *
13290 -ATTTTTTGGTGTTAGCCATGCAATAGCTGATACCCCTTTTTTGAGAAAAAAAAATTTC
1 AATTTTTTTGTGTTGGCCATGCAATAGCCGACACCCCTTTTTTGAGAAAAAAAAATTGC
* *
13348 AAAATTTTTTTGTGTTGGCCATGCAATGGCCGACACTCCCTTTTTT-AGAAAAAAAAATTTC
1 --AATTTTTTTGTGTTGGCCATGCAATAGCCGACAC-CCCTTTTTTGAGAAAAAAAAATTGC
* * * * * * * *
13409 AAAATTTTTTGGTGTTGACAACGCAATCGCTGACACCCCCTTTTCTCG-G-ATAAAAAATTGC
1 --AATTTTTTTGTGTTGGCCATGCAATAGCCGACA-CCCCTTTT-TTGAGAAAAAAAAATTGC
**
13470 -ATTTTTGAGTGTTGGCCAT
1 AATTTTTTTGTGTTGGCCAT
13489 TGCATGACCA
Statistics
Matches: 164, Mismatches: 27, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
57 3 0.02
58 26 0.16
59 3 0.02
60 31 0.19
61 89 0.54
62 12 0.07
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (59 bp):
AATTTTTTTGTGTTGGCCATGCAATAGCCGACACCCCTTTTTTGAGAAAAAAAAATTGC
Found at i:13369 original size:61 final size:61
Alignment explanation
Indices: 13229--13452 Score: 242
Period size: 61 Copynumber: 3.7 Consensus size: 61
13219 ATATATATAT
* * * *
13229 AATTTTTTTGTGTTGGCCATACAATGGCCGACACCCCTATTTATCTGA-TAAAAAAAATTGC--
1 AATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCT-TTT-T-TGAGAAAAAAAAATTTCAA
* * * *
13290 -ATTTTTTGGTGTTAGCCATGCAATAGCTGATACCCCTTTTTTGAGAAAAAAAAATTTCAA
1 AATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTGAGAAAAAAAAATTTCAA
*
13350 AATTTTTTTGTGTTGGCCATGCAATGGCCGACACTCCCTTTTTT-AGAAAAAAAAATTTCAA
1 AATTTTTTGGTGTTGGCCATGCAATGGCCGACAC-CCCTTTTTTGAGAAAAAAAAATTTCAA
* * * * * *
13411 AATTTTTTGGTGTTGACAACGCAATCGCTGACACCCCCTTTT
1 AATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTT
13453 CTCGGATAAA
Statistics
Matches: 138, Mismatches: 20, Indels: 11
0.82 0.12 0.07
Matches are distributed among these distances:
57 3 0.02
58 12 0.09
59 3 0.02
60 38 0.28
61 73 0.53
62 9 0.07
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (61 bp):
AATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTGAGAAAAAAAAATTTCAA
Found at i:15212 original size:12 final size:12
Alignment explanation
Indices: 15189--15218 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
15179 GTAAGTTTTT
15189 TTTCTT-CTTCC
1 TTTCTTCCTTCC
15200 TTTCTTCCTTCC
1 TTTCTTCCTTCC
15212 TTTCTTC
1 TTTCTTC
15219 ATAAAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTCTTCCTTCC
Found at i:21135 original size:61 final size:61
Alignment explanation
Indices: 21062--21206 Score: 281
Period size: 61 Copynumber: 2.4 Consensus size: 61
21052 AAACCTCTAG
21062 TTGGATCCAAATTAAATTCTAAAAAGATAATTAGAATTAAATATAAACAATACTTCCCTAA
1 TTGGATCCAAATTAAATTCTAAAAAGATAATTAGAATTAAATATAAACAATACTTCCCTAA
21123 TTGGATCCAAATTAAATTCTAAAAAGATAATTAGAATTAAATATAAACAATACTTCCCTAA
1 TTGGATCCAAATTAAATTCTAAAAAGATAATTAGAATTAAATATAAACAATACTTCCCTAA
*
21184 TTGGATCCAAATTAAACTCTAAA
1 TTGGATCCAAATTAAATTCTAAA
21207 TTATAAAGCC
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 83 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (61 bp):
TTGGATCCAAATTAAATTCTAAAAAGATAATTAGAATTAAATATAAACAATACTTCCCTAA
Found at i:28776 original size:12 final size:11
Alignment explanation
Indices: 28758--28794 Score: 58
Period size: 12 Copynumber: 3.4 Consensus size: 11
28748 AATTTTTCCC
28758 TTTTTTATTAT
1 TTTTTTATTAT
28769 TCTTTTTATTAT
1 T-TTTTTATTAT
28781 TTTTTT-TTAT
1 TTTTTTATTAT
28791 TTTT
1 TTTT
28795 ATGTTCAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 8 0.32
11 6 0.24
12 11 0.44
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTATTAT
Found at i:31827 original size:2 final size:2
Alignment explanation
Indices: 31820--31861 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
31810 TACTACTTTG
31820 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
31862 GTCTATGATA
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:36239 original size:56 final size:56
Alignment explanation
Indices: 36173--36284 Score: 170
Period size: 56 Copynumber: 2.0 Consensus size: 56
36163 TACAATAACT
* * * **
36173 ATTATTATTGTTCTTTCATGGTTACATGTGTTAAAGATGCTATGTTAGAATGTTTG
1 ATTATTATTGTTATTTCAGGGTTACATATGTTAAAGACACTATGTTAGAATGTTTG
*
36229 ATTATTATTGTTATTTCAGGGTTATATATGTTAAAGACACTATGTTAGAATGTTTG
1 ATTATTATTGTTATTTCAGGGTTACATATGTTAAAGACACTATGTTAGAATGTTTG
36285 CTTAAGAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (56 bp):
ATTATTATTGTTATTTCAGGGTTACATATGTTAAAGACACTATGTTAGAATGTTTG
Found at i:40031 original size:17 final size:18
Alignment explanation
Indices: 39999--40032 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39989 TTATAAAAAA
*
39999 AAATTTTAGTTGGGTTTT
1 AAATTTTAGATGGGTTTT
40017 AAATTTTA-ATGGGTTT
1 AAATTTTAGATGGGTTT
40033 GGATTTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (18 bp):
AAATTTTAGATGGGTTTT
Found at i:40056 original size:16 final size:18
Alignment explanation
Indices: 40037--40073 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40027 GGGTTTGGAT
40037 TTTTAGGA-GTA-TTAAG
1 TTTTAGGAGGTATTTAAG
*
40053 TTTTAGTAGGTATTTAAG
1 TTTTAGGAGGTATTTAAG
40071 TTT
1 TTT
40074 AAAGTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (18 bp):
TTTTAGGAGGTATTTAAG
Found at i:48380 original size:24 final size:24
Alignment explanation
Indices: 48353--48400 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
48343 AACAATTAAA
*
48353 ATGAGACTTG-GATGTGAAATGAAT
1 ATGAGACTTGAGATG-GAAAAGAAT
*
48377 ATGAGATTTGAGATGGAAAAGAAT
1 ATGAGACTTGAGATGGAAAAGAAT
48401 TAAGCTTAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.42, C:0.02, G:0.29, T:0.27
Consensus pattern (24 bp):
ATGAGACTTGAGATGGAAAAGAAT
Found at i:61234 original size:15 final size:15
Alignment explanation
Indices: 61202--61235 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
61192 GACAAAGACA
*
61202 ACGACAACGACAACG
1 ACGACAACGACAAAG
*
61217 ACGACAACGATAAAG
1 ACGACAACGACAAAG
61232 ACGA
1 ACGA
61236 GCTACTTCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.26, G:0.21, T:0.03
Consensus pattern (15 bp):
ACGACAACGACAAAG
Found at i:63962 original size:11 final size:11
Alignment explanation
Indices: 63948--63987 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
63938 GTCAATATAA
63948 TAGCAAAATGG
1 TAGCAAAATGG
**
63959 TAGCAAAATAA
1 TAGCAAAATGG
*
63970 TATCAAAATGG
1 TAGCAAAATGG
63981 TAGCAAA
1 TAGCAAA
63988 CATCAATGAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.20
Consensus pattern (11 bp):
TAGCAAAATGG
Found at i:63999 original size:22 final size:22
Alignment explanation
Indices: 63944--63987 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
63934 TAATGTCAAT
*
63944 ATAATAGCAAAATGGTAGCAAA
1 ATAATATCAAAATGGTAGCAAA
63966 ATAATATCAAAATGGTAGCAAA
1 ATAATATCAAAATGGTAGCAAA
63988 CATCAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.55, C:0.09, G:0.16, T:0.20
Consensus pattern (22 bp):
ATAATATCAAAATGGTAGCAAA
Found at i:66260 original size:22 final size:22
Alignment explanation
Indices: 66235--66276 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
66225 TTTTGCCTTT
* *
66235 TTCTAATTTTGCTGTTATTATC
1 TTCTAATTCTGCTGCTATTATC
*
66257 TTCTGATTCTGCTGCTATTA
1 TTCTAATTCTGCTGCTATTA
66277 ATTCTGAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.55
Consensus pattern (22 bp):
TTCTAATTCTGCTGCTATTATC
Done.