Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012836.1 Kokia drynarioides strain JFW-HI SEQ_127849, 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: 21871
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Warning! 73 characters in sequence are not A, C, G, or T
Found at i:559 original size:26 final size:26
Alignment explanation
Indices: 529--704 Score: 224
Period size: 26 Copynumber: 7.1 Consensus size: 26
519 GCTTACTGTT
* *
529 CAGCACTATGTGTGCTTATGTTTCTC
1 CAGCACTATGTGTGCTTCTGTTTCCC
* *
555 CAGCACTGTGTGTGCTTCTGTTTCTC
1 CAGCACTATGTGTGCTTCTGTTTCCC
581 CAGCACTATGTGTGCTTCTGTTTCCC
1 CAGCACTATGTGTGCTTCTGTTTCCC
*
607 CAGCACTATGTGTGCTTCTATTTCCC
1 CAGCACTATGTGTGCTTCTGTTTCCC
633 CAGCACTATGTGTGCTTCTG-TT---
1 CAGCACTATGTGTGCTTCTGTTTCCC
* *
655 CAGCACTGTGTGTGTTTCTG-TT---
1 CAGCACTATGTGTGCTTCTGTTTCCC
*
677 CAGCACTGTGTGTGCTTCTGTTTCCC
1 CAGCACTATGTGTGCTTCTGTTTCCC
703 CA
1 CA
705 ACAGTTATGT
Statistics
Matches: 137, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
22 39 0.28
23 2 0.01
25 2 0.01
26 94 0.69
ACGTcount: A:0.12, C:0.27, G:0.21, T:0.40
Consensus pattern (26 bp):
CAGCACTATGTGTGCTTCTGTTTCCC
Found at i:3102 original size:56 final size:56
Alignment explanation
Indices: 3014--3174 Score: 243
Period size: 56 Copynumber: 2.9 Consensus size: 56
3004 TCATCTTCTT
3014 CCATATGATGCCATAGCCACC-TGACTAGGTCTTACACTATATGGTCTTCATTTCC
1 CCATATGATGCCATAGCCACCATGACTAGGTCTTACACTATATGGTCTTCATTTCC
* * * * * *
3069 TCATATGTTTCCATAGTCACCATGACTAGGTCTTACACTATATTGTCTTCTTTTCC
1 CCATATGATGCCATAGCCACCATGACTAGGTCTTACACTATATGGTCTTCATTTCC
* *
3125 CCATATGATGCCATAACCACCATGACTAGGACTTACACTATATGGTCTTC
1 CCATATGATGCCATAGCCACCATGACTAGGTCTTACACTATATGGTCTTC
3175 GATTGCCATG
Statistics
Matches: 92, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
55 17 0.18
56 75 0.82
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (56 bp):
CCATATGATGCCATAGCCACCATGACTAGGTCTTACACTATATGGTCTTCATTTCC
Found at i:4799 original size:18 final size:18
Alignment explanation
Indices: 4770--4854 Score: 116
Period size: 18 Copynumber: 4.7 Consensus size: 18
4760 CTCTTGTGAT
**
4770 CCAGTAATGCTCTTACGAG
1 CCAGT-ATGCTCAAACGAG
*
4789 CTAGTATGCTCAAACGAG
1 CCAGTATGCTCAAACGAG
*
4807 CCAGTATGCTCAAATGAG
1 CCAGTATGCTCAAACGAG
*
4825 CCAGTATTCTCAAACGAG
1 CCAGTATGCTCAAACGAG
4843 CCAGTATGCTCA
1 CCAGTATGCTCA
4855 TTCTTCCATA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
18 54 0.93
19 4 0.07
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24
Consensus pattern (18 bp):
CCAGTATGCTCAAACGAG
Found at i:21078 original size:30 final size:29
Alignment explanation
Indices: 21027--21255 Score: 176
Period size: 29 Copynumber: 7.8 Consensus size: 29
21017 ACTCGGGGGC
* *
21027 AAAATGGTAATTTTTACAAGTTTCGAGATCA
1 AAAATGG-AATTTTTAGAAGTTTCGAGGT-A
* * *
21058 AAAAAGGAATTTTTGGAAGTTT-GGGGTA
1 AAAATGGAATTTTTAGAAGTTTCGAGGTA
* * *
21086 AAAATGTAATTTTTAGAAATTTCAAGGTTA
1 AAAATGGAATTTTTAGAAGTTTCGAGG-TA
* *
21116 AAAATGGAATTTTTGGAAGTTT-AAGGGTA
1 AAAATGGAATTTTTAGAAGTTTCGA-GGTA
* * *
21145 AAAATGTAATTTTTGGAAGTCTCGAGGTTA
1 AAAATGGAATTTTTAGAAGTTTCGAGG-TA
* * * * *
21175 AAATTGGAATTTTCAAAAGTTTAGGGGTA
1 AAAATGGAATTTTTAGAAGTTTCGAGGTA
* *
21204 AAAATGTAATTTTTGGAAGTTT-GAGGGTA
1 AAAATGGAATTTTTAGAAGTTTCGA-GGTA
* *
21233 AAAATGTAATTTTTGGATAGTTT
1 AAAATGGAATTTTTAGA-AGTTT
21256 AGAGACCTCC
Statistics
Matches: 160, Mismatches: 31, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
28 20 0.12
29 71 0.44
30 63 0.39
31 6 0.04
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTAGAAGTTTCGAGGTA
Found at i:21118 original size:29 final size:28
Alignment explanation
Indices: 21065--21256 Score: 186
Period size: 29 Copynumber: 6.6 Consensus size: 28
21055 TCAAAAAAGG
**
21065 AATTTTTGGAAGTTTGGGGTAAAAATGT
1 AATTTTTGGAAGTTTAAGGTAAAAATGT
* * *
21093 AATTTTTAGAAATTTCAAGGTTAAAAATGG
1 AATTTTTGGAAGTTT-AAGG-TAAAAATGT
21123 AATTTTTGGAAGTTTAAGGGTAAAAATGT
1 AATTTTTGGAAGTTTAA-GGTAAAAATGT
** * *
21152 AATTTTTGGAAGTCTCGAGGTTAAAATTGG
1 AATTTTTGGAAGT-TTAAGG-TAAAAATGT
*** *
21182 AATTTTCAAAAGTTTAGGGGTAAAAATGT
1 AATTTTTGGAAGTTTA-AGGTAAAAATGT
*
21211 AATTTTTGGAAGTTTGAGGGTAAAAATGT
1 AATTTTTGGAAGTTT-AAGGTAAAAATGT
21240 AATTTTTGGATAGTTTA
1 AATTTTTGGA-AGTTTA
21257 GAGACCTCCA
Statistics
Matches: 133, Mismatches: 23, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
28 13 0.10
29 70 0.53
30 50 0.38
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (28 bp):
AATTTTTGGAAGTTTAAGGTAAAAATGT
Found at i:21173 original size:59 final size:59
Alignment explanation
Indices: 21027--21257 Score: 286
Period size: 59 Copynumber: 3.9 Consensus size: 59
21017 ACTCGGGGGC
* * * *
21027 AAAATGGTAATTTTTACAAGTTTCGAGATCAAAAAAGGAATTTTTGGAAGTTT-GGGGTA
1 AAAAT-GTAATTTTTAGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAGTTTAGGGGTA
* * *
21086 AAAATGTAATTTTTAGAAATTTCAAGGTTAAAAATGGAATTTTTGGAAGTTTAAGGGTA
1 AAAATGTAATTTTTAGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAGTTTAGGGGTA
* * * ***
21145 AAAATGTAATTTTTGGAAGTCTCGAGGTTAAAATTGGAATTTTCAAAAGTTTAGGGGTA
1 AAAATGTAATTTTTAGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAGTTTAGGGGTA
* * *
21204 AAAATGTAATTTTTGGAAGTTT-GAGGGTAAAAATGTAATTTTTGGATAGTTTAG
1 AAAATGTAATTTTTAGAAGTTTCGAGGTTAAAAATGGAATTTTTGGA-AGTTTAG
21258 AGACCTCCAG
Statistics
Matches: 147, Mismatches: 23, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
58 59 0.40
59 88 0.60
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (59 bp):
AAAATGTAATTTTTAGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAGTTTAGGGGTA
Found at i:21178 original size:88 final size:87
Alignment explanation
Indices: 21065--21254 Score: 249
Period size: 88 Copynumber: 2.2 Consensus size: 87
21055 TCAAAAAAGG
* * * * *
21065 AATTTTTGGAAGTTTGGGGTAAAAA-TGTAATTTTTAGAAA-TTTCAAGGTTAAAAATGGAATTT
1 AATTTTTGGAAGTTCGAGGTAAAAATTGGAATTTTCA-AAAGTTT-AAGGGTAAAAATGGAATTT
21128 TTGGAAGTTTAAGGGTAAAAATGT
64 TTGGAAGTTTAAGGGTAAAAATGT
* * *
21152 AATTTTTGGAAGTCTCGAGGTTAAAATTGGAATTTTCAAAAGTTTAGGGGTAAAAATGTAATTTT
1 AATTTTTGGAAGT-TCGAGGTAAAAATTGGAATTTTCAAAAGTTTAAGGGTAAAAATGGAATTTT
*
21217 TGGAAGTTTGAGGGTAAAAATGT
65 TGGAAGTTTAAGGGTAAAAATGT
21240 AATTTTTGGATAGTT
1 AATTTTTGGA-AGTT
21255 TAGAGACCTC
Statistics
Matches: 90, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
87 13 0.14
88 62 0.69
89 15 0.17
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (87 bp):
AATTTTTGGAAGTTCGAGGTAAAAATTGGAATTTTCAAAAGTTTAAGGGTAAAAATGGAATTTTT
GGAAGTTTAAGGGTAAAAATGT
Done.