Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013610.1 Kokia drynarioides strain JFW-HI SEQ_128637, 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: 5640
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Found at i:3930 original size:27 final size:27
Alignment explanation
Indices: 3891--3950 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
3881 AACTTTCAAC
* *
3891 TAATGATTGTTTCCTTTGATCCTCTTTT
1 TAAT-ATTATTTCCTTTGATCCTCTTCT
*
3919 TAATATTATTTCTTTTGATCCTCTTCT
1 TAATATTATTTCCTTTGATCCTCTTCT
3946 TAATA
1 TAATA
3951 AAATTTTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.57
Consensus pattern (27 bp):
TAATATTATTTCCTTTGATCCTCTTCT
Found at i:3956 original size:27 final size:27
Alignment explanation
Indices: 3900--3956 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
3890 CTAATGATTG
* **
3900 TTTCCTTTGATCCTCTTTTTAATATTA
1 TTTCCTTTGATCCTCTTCTTAATAAAA
*
3927 TTTCTTTTGATCCTCTTCTTAATAAAA
1 TTTCCTTTGATCCTCTTCTTAATAAAA
3954 TTT
1 TTT
3957 TTGAAATACG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.21, C:0.18, G:0.04, T:0.58
Consensus pattern (27 bp):
TTTCCTTTGATCCTCTTCTTAATAAAA
Found at i:4890 original size:206 final size:199
Alignment explanation
Indices: 4530--5191 Score: 661
Period size: 206 Copynumber: 3.3 Consensus size: 199
4520 TCCCAGCTTA
* * *
4530 AAGCAGATCGGAGCAATAAACAGCTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAATTCATC
1 AAGCA-ATCGGAGCAATAAACGGTTAGCTTCCTGATGAGATAC-GAGAAGTGAACCAAATTCGTC
*
4595 TTCCTGGTGAGATACAGAGAAGCGGATTGAAACAAGCTATACGGTCATCTTCCTGATGAGATACT
64 TTCCTGGTGAGATACAGAGAAGCGGATTGAAACAAGCGATACGGTCATCTTCCTGATGAGATACT
* * * * * * *
4660 GAGAAGA-AGACCAAGTCAAACCCACGCTCGAAGTG-AGCAAGTCTTCGAATCTCAGCTTCCTGA
129 GAGAAGAGA-ACCAAATCAAACCCACGCTCAAAGCGAAGAAAATCTTCGAACCCCAGCTTCC---
4723 TGAGACACCGAG
190 TGAGA-ACC-AG
* *
4735 AAGCAAATCGGAGCAATAAACGGTTTGCTTCCTGATGAGATACGAAGAAGTAAACCAAAATTCGT
1 AAGC-AATCGGAGCAATAAACGGTTAGCTTCCTGATGAGATACG-AGAAGTGAACC-AAATTCGT
* * *
4800 CTTCCTGGTAAGATACAGAGAGGCGGATTGAAACAAGCGATACGGTCATCTTCCTGACGAGATAC
63 CTTCCTGGTGAGATACAGAGAAGCGGATTGAAACAAGCGATACGGTCATCTTCCTGATGAGATAC
* * *
4865 TGGGAAGAGAACCAAATCGAACCCACGCTCAAAGCGAATAAAATCTTCGAACCCCAGCTTCCTGA
128 TGAGAAGAGAACCAAATCAAACCCACGCTCAAAGCGAAGAAAATCTTCGAACCCCAGCTTCCTGA
*
4930 GAAGCAG
193 GAACCAG
* * * *
4937 --G---TCGAAGAAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCT
1 AAGCAATCGGAGCAATAAACGGTTAGCTTCCTGATGAGATAC-GAGAAGTGAACCAAATTCGTCT
* * * ** *
4997 TCCTGATGAGATACAGAGAAGC-AAGTTGAAACAAACGACGCGGTCATCTTCCTGATGAGACACT
65 TCCTGGTGAGATACAGAGAAGCGGA-TTGAAACAAGCGATACGGTCATCTTCCTGATGAGATACT
* * * *
5061 GAGAAGA-AGACC----CAAA-CGAGGCTCAAAACGAA-CAAATCTTCGAACCCCAGCTTCCTGA
129 GAGAAGAGA-ACCAAATCAAACCCACGCTCAAAGCGAAGAAAATCTTCGAACCCCAGCTTCCTGA
*
5119 TGAGACGTTGAG
193 -GA-AC---CAG
* * * * *
5131 AAGCAGGTCGAAGCCATAAAGTGGTTAGCTCCCTGATGAGATACAGAGAAGTGAACCAAAT
1 AAGCA-ATCGGAGCAATAAA-CGGTTAGCTTCCTGATGAGATAC-GAGAAGTGAACCAAAT
5192 CCTGATGAAA
Statistics
Matches: 389, Mismatches: 48, Indels: 44
0.81 0.10 0.09
Matches are distributed among these distances:
189 25 0.06
190 15 0.04
191 4 0.01
194 4 0.01
195 71 0.18
196 43 0.11
197 1 0.00
200 12 0.03
201 37 0.10
202 2 0.01
203 2 0.01
204 6 0.02
205 48 0.12
206 98 0.25
207 21 0.05
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (199 bp):
AAGCAATCGGAGCAATAAACGGTTAGCTTCCTGATGAGATACGAGAAGTGAACCAAATTCGTCTT
CCTGGTGAGATACAGAGAAGCGGATTGAAACAAGCGATACGGTCATCTTCCTGATGAGATACTGA
GAAGAGAACCAAATCAAACCCACGCTCAAAGCGAAGAAAATCTTCGAACCCCAGCTTCCTGAGAA
CCAG
Found at i:5581 original size:17 final size:17
Alignment explanation
Indices: 5559--5640 Score: 92
Period size: 17 Copynumber: 4.8 Consensus size: 17
5549 CAAACTCGCT
5559 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
5576 TTAAATTTGTTTAAAAA
1 TTAAATTTATTTTAAAA
*
5593 TTTAAATTTATTTTAAAT
1 -TTAAATTTATTTTAAAA
* **
5611 TTAAATTTAATTTAAGT
1 TTAAATTTATTTTAAAA
*
5628 TTAAAATTATTTT
1 TTAAATTTATTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
17 41 0.75
18 14 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:5599 original size:6 final size:6
Alignment explanation
Indices: 5590--5632 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
5580 ATTTGTTTAA
* *
5590 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT AAGTTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAA
5633 ATTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 9 0.29
6 22 0.71
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:5635 original size:35 final size:34
Alignment explanation
Indices: 5558--5640 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 34
5548 CCAAACTCGC
*
5558 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAAATTAAATTTATTT-AAAA
* *
5593 TTTAAATTTATTTTAAATTTAAATTTAATTT-AAG
1 TTTAAATTTATTTTAAAATTAAATTT-ATTTAAAA
*
5627 TTTAAAATTATTTT
1 TTTAAATTTATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
34 15 0.35
35 25 0.58
36 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (34 bp):
TTTAAATTTATTTTAAAATTAAATTTATTTAAAA
Done.