Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009048.1 Kokia drynarioides strain JFW-HI SEQ_123747, 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: 11198
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Found at i:2655 original size:93 final size:92
Alignment explanation
Indices: 2496--2771 Score: 419
Period size: 93 Copynumber: 3.0 Consensus size: 92
2486 ATCATGGTCG
* *
2496 GCAGAAGAAATCATTTCAGAAGCAACCAGGCCCTCACCACTGGGCTCTGTTTCTTTAGCTTGCAT
1 GCAGAAGAAATCATTTCAGAAGCAACCTGGCCCTCACCACTGGGCTCAG-TTCTTTAGCTTGCAT
*
2561 AAAATGTTCGGCATGAGTTGTAACATCT
65 AAAATGTTCAGCATGAGTTGTAACATCT
* *
2589 GCAGAAGAAATCATTTGAGAAGCAACCTGGCCCTCACCACTGGGCTCAGCTTCTTTGGCTTGCAT
1 GCAGAAGAAATCATTTCAGAAGCAACCTGGCCCTCACCACTGGGCTCAG-TTCTTTAGCTTGCAT
2654 AAAATGTTCAGCATGAGTTGTAACATCT
65 AAAATGTTCAGCATGAGTTGTAACATCT
* * * *
2682 GCAGAAGAAATCATTTTAGAAGCAACCTGGGCCTCAACACTGGCCTCTA-TTCCTTTAGCTTGCA
1 GCAGAAGAAATCATTTCAGAAGCAACCTGGCCCTCACCACTGGGCTC-AGTT-CTTTAGCTTGCA
*
2746 TAAAATGTTCCGCATGAGTTGTAACA
64 TAAAATGTTCAGCATGAGTTGTAACA
2772 CCACCATATA
Statistics
Matches: 169, Mismatches: 12, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
92 2 0.01
93 166 0.98
94 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (92 bp):
GCAGAAGAAATCATTTCAGAAGCAACCTGGCCCTCACCACTGGGCTCAGTTCTTTAGCTTGCATA
AAATGTTCAGCATGAGTTGTAACATCT
Found at i:3796 original size:186 final size:181
Alignment explanation
Indices: 3485--3822 Score: 561
Period size: 186 Copynumber: 1.8 Consensus size: 181
3475 TATTAGAACC
3485 CTTAGTATTAGGCTGGACTTCAGTACTTCTCAGTTGAGTAGTGCCTTCTCCTTTGCTTAAAGATA
1 CTTAGTATTAGGCTGGACTTCAGTACTTCT-A-TTGAGTAGTGCCTTCTCCTTTGCTTAAAGATA
* *
3550 GATTCAAGGAAACAGTCTTTTCCTGACTCCGAAAACCTTGCTCATTATTTCCGCTAGCCATAGCT
64 AATTCAAGGAAACAGTCTTTTCCTGACTCCGAAAACCTTGCTCATTATTTCCGCTAGCCATAACT
3615 GAAGGATATTCCCTTAAACCTAATAGGCTCATACCAAGCTTTCCTTTGCTACA
129 GAAGGATATTCCCTTAAACCTAATAGGCTCATACCAAGCTTTCCTTTGCTACA
3668 CTTAGTATTAGGCTGGACTTCAGTACTTCT-TTGAGTAGTGCCTTCTCCTTTGCTTAAAGATAAA
1 CTTAGTATTAGGCTGGACTTCAGTACTTCTATTGAGTAGTGCCTTCTCCTTTGCTTAAAGATAAA
* *
3732 TTCAAGGAAACAGGTTCAGTCTTTTCCTGATTCCGAAAACCTTGCTCATTATTTCTGCTAGCCAT
66 TTCAAGG-AA-A----CAGTCTTTTCCTGACTCCGAAAACCTTGCTCATTATTTCCGCTAGCCAT
3797 AACTGAAGGATATTCCCTTAAACCTA
125 AACTGAAGGATATTCCCTTAAACCTA
3823 GGGATAATCC
Statistics
Matches: 145, Mismatches: 4, Indels: 9
0.92 0.03 0.06
Matches are distributed among these distances:
180 40 0.28
181 2 0.01
182 1 0.01
183 30 0.21
186 72 0.50
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.34
Consensus pattern (181 bp):
CTTAGTATTAGGCTGGACTTCAGTACTTCTATTGAGTAGTGCCTTCTCCTTTGCTTAAAGATAAA
TTCAAGGAAACAGTCTTTTCCTGACTCCGAAAACCTTGCTCATTATTTCCGCTAGCCATAACTGA
AGGATATTCCCTTAAACCTAATAGGCTCATACCAAGCTTTCCTTTGCTACA
Found at i:4626 original size:27 final size:27
Alignment explanation
Indices: 4554--4627 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
4544 ACTCGCTACG
*
4554 ACACCACTGGTGTTAGAACTGGCTAAA
1 ACACCAGTGGTGTTAGAACTGGCTAAA
* * *
4581 GCATC-GCTGGTGTTCGAACTGGCTAAA
1 ACACCAG-TGGTGTTAGAACTGGCTAAA
4608 ACACCAGTGGGTGTT-GAACT
1 ACACCAGT-GGTGTTAGAACT
4628 CACTGCAACA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 31 0.82
28 7 0.18
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (27 bp):
ACACCAGTGGTGTTAGAACTGGCTAAA
Found at i:5608 original size:25 final size:26
Alignment explanation
Indices: 5562--5610 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
5552 AAAAAAGCAA
*
5562 AAAAAAATCTACAAGATTAGAAGAAG
1 AAAAAAATCTACAAGATCAGAAGAAG
**
5588 AAAAAAA-CTACCTGATCAGAAGA
1 AAAAAAATCTACAAGATCAGAAGA
5611 GGCGAGGAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.59, C:0.12, G:0.14, T:0.14
Consensus pattern (26 bp):
AAAAAAATCTACAAGATCAGAAGAAG
Done.