Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014327.1 Kokia drynarioides strain JFW-HI SEQ_129364, 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: 30742
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:26 original size:15 final size:15
Alignment explanation
Indices: 6--38 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1 TAAAT
*
6 ATTATTATTAATTTC
1 ATTATTATTAATGTC
21 ATTATTATTAATGTC
1 ATTATTATTAATGTC
36 ATT
1 ATT
39 TATTGTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (15 bp):
ATTATTATTAATGTC
Found at i:688 original size:17 final size:17
Alignment explanation
Indices: 668--714 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
658 AAATGAATTT
*
668 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* *
685 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
702 TAAATTTAAATTT
1 TAAATTTAAATTT
715 GTTGGGCCCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:1304 original size:32 final size:32
Alignment explanation
Indices: 1258--1327 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
1248 TAAAACTCAA
1258 AACCAAAATAGATTAATTAGTTATCATGCTAT
1 AACCAAAATAGATTAATTAGTTATCATGCTAT
*
1290 AACCAAAATGGATTAATTAGTTATCATGCTAT
1 AACCAAAATAGATTAATTAGTTATCATGCTAT
1322 AACCAA
1 AACCAA
1328 TCTTTTAGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.31
Consensus pattern (32 bp):
AACCAAAATAGATTAATTAGTTATCATGCTAT
Found at i:3720 original size:24 final size:24
Alignment explanation
Indices: 3693--3750 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
3683 CTTATGGGCA
*
3693 AGCGCCGCTAAAGGTCAAAGCAAT
1 AGCGGCGCTAAAGGTCAAAGCAAT
**
3717 AGCGGCGCCTAAAGGTCAGGGCAAT
1 AGCGGCG-CTAAAGGTCAAAGCAAT
3742 AGCGGCGCT
1 AGCGGCGCT
3751 TATAGGCAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 8 0.27
25 22 0.73
ACGTcount: A:0.29, C:0.26, G:0.33, T:0.12
Consensus pattern (24 bp):
AGCGGCGCTAAAGGTCAAAGCAAT
Found at i:3729 original size:25 final size:25
Alignment explanation
Indices: 3700--3749 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3690 GCAAGCGCCG
3700 CTAAAGGTCAAAGCAATAGCGGCGC
1 CTAAAGGTCAAAGCAATAGCGGCGC
**
3725 CTAAAGGTCAGGGCAATAGCGGCGC
1 CTAAAGGTCAAAGCAATAGCGGCGC
3750 TTATAGGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.24, G:0.32, T:0.12
Consensus pattern (25 bp):
CTAAAGGTCAAAGCAATAGCGGCGC
Found at i:3771 original size:66 final size:66
Alignment explanation
Indices: 3661--3786 Score: 189
Period size: 66 Copynumber: 1.9 Consensus size: 66
3651 TTAACGCCAC
* *
3661 AAAGGTCAAAGCAATAACGGTGCTTATGGGCAAGCGCCGCTAAAGGTCAAAGCAATAGCGGCGCC
1 AAAGGTCAAAGCAATAACGGCGCTTATAGGCAAGCGCCGCTAAAGGTCAAAGCAATAGCGGCGCC
3726 T
66 T
** * * *
3727 AAAGGTCAGGGCAATAGCGGCGCTTATAGGCAAGCGCCGTTAAAGGTCAGAGCAATAGCG
1 AAAGGTCAAAGCAATAACGGCGCTTATAGGCAAGCGCCGCTAAAGGTCAAAGCAATAGCG
3787 ACACTTATGC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.33, C:0.21, G:0.31, T:0.15
Consensus pattern (66 bp):
AAAGGTCAAAGCAATAACGGCGCTTATAGGCAAGCGCCGCTAAAGGTCAAAGCAATAGCGGCGCC
T
Found at i:3776 original size:41 final size:41
Alignment explanation
Indices: 3725--3840 Score: 146
Period size: 41 Copynumber: 2.9 Consensus size: 41
3715 ATAGCGGCGC
* * * *
3725 CTAAAGGTCAGGGCAATAGCGGCGCTTATAG-GCAAGCGCCG
1 CTAAAGGTCAGAGCAATAGCGACGCTTAT-GCGAAAGCACCG
* *
3766 TTAAAGGTCAGAGCAATAGCGACACTTATGCGAAAGCACCG
1 CTAAAGGTCAGAGCAATAGCGACGCTTATGCGAAAGCACCG
*
3807 CTAAAGGTCAGAGCAATTGCGACGCTTATG-GAAA
1 CTAAAGGTCAGAGCAATAGCGACGCTTATGCGAAA
3841 AAACGCCGCT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
40 5 0.08
41 60 0.92
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (41 bp):
CTAAAGGTCAGAGCAATAGCGACGCTTATGCGAAAGCACCG
Found at i:9822 original size:37 final size:37
Alignment explanation
Indices: 9766--9839 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
9756 GACTATGTTT
**
9766 TTTAACGGTATTTGCGGGAAAATTGCTGTTAAAGATC
1 TTTAACGGTATTTGCGGGAAAAGCGCTGTTAAAGATC
* * * *
9803 TTTAATGGTGTTTGTGGGAAAAGCGTTGTTAAAGATC
1 TTTAACGGTATTTGCGGGAAAAGCGCTGTTAAAGATC
9840 ATGTTCTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.36
Consensus pattern (37 bp):
TTTAACGGTATTTGCGGGAAAAGCGCTGTTAAAGATC
Found at i:9902 original size:43 final size:43
Alignment explanation
Indices: 9810--9913 Score: 131
Period size: 43 Copynumber: 2.4 Consensus size: 43
9800 ATCTTTAATG
* * * *
9810 GTGTTTGTGGGAAAAGCGTTGTTAAAGATCATGTTCTTTAGCG
1 GTGTTTGTCGGAAAAGCGTCGTTAAAGATCATGTACTTTAGCA
*
9853 GCGTTTG-CGGAATAAGCGTCGTTAAAGATCATGTACTTTAGCA
1 GTGTTTGTCGGAA-AAGCGTCGTTAAAGATCATGTACTTTAGCA
9896 GTGTTTGT-GAGAAAAGCG
1 GTGTTTGTCG-GAAAAGCG
9914 CTAGGATAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
42 4 0.08
43 45 0.87
44 3 0.06
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.33
Consensus pattern (43 bp):
GTGTTTGTCGGAAAAGCGTCGTTAAAGATCATGTACTTTAGCA
Found at i:9999 original size:42 final size:43
Alignment explanation
Indices: 9921--10037 Score: 139
Period size: 42 Copynumber: 2.7 Consensus size: 43
9911 GCGCTAGGAT
*
9921 AAGTGTCGCTAAAGACCATGGTT-TGTAGCGACGTTTGTG-GAA
1 AAGTGTCGCTAAAGACCAT-GTTCTTTAGCGACGTTTGTGAGAA
* * ** *
9963 AAGTGCCGCTAAAGACCATGTTCTTTAGTGGGGTTTGTGAGAT
1 AAGTGTCGCTAAAGACCATGTTCTTTAGCGACGTTTGTGAGAA
* *
10006 CAGCGTCGCTAAAGACCATGTTCTTTAGCGAC
1 AAGTGTCGCTAAAGACCATGTTCTTTAGCGAC
10038 ATTTTTGGGA
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
41 3 0.05
42 30 0.49
43 28 0.46
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (43 bp):
AAGTGTCGCTAAAGACCATGTTCTTTAGCGACGTTTGTGAGAA
Found at i:11834 original size:6 final size:6
Alignment explanation
Indices: 11825--11854 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
11815 AAAAAGGAAG
11825 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
11855 TGGAAGTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:14626 original size:5 final size:5
Alignment explanation
Indices: 14616--14640 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
14606 CAAAAGAAGT
14616 GGAGG GGAGG GGAGG GGAGG GGAGG
1 GGAGG GGAGG GGAGG GGAGG GGAGG
14641 ACAGGGGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (5 bp):
GGAGG
Found at i:15599 original size:16 final size:16
Alignment explanation
Indices: 15551--15599 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
15541 TATTATTTTG
15551 AATTATAAGTAAGAAA
1 AATTATAAGTAAGAAA
* *** *
15567 AATTCTACCAAAAAAA
1 AATTATAAGTAAGAAA
15583 AATTATAAGTAAGAAA
1 AATTATAAGTAAGAAA
15599 A
1 A
15600 TTTAACTTAT
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.63, C:0.06, G:0.08, T:0.22
Consensus pattern (16 bp):
AATTATAAGTAAGAAA
Done.