Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013641.1 Kokia drynarioides strain JFW-HI SEQ_128669, 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: 26884
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Found at i:1928 original size:30 final size:30
Alignment explanation
Indices: 1837--1929 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 30
1827 AAAGTCCATT
* *
1837 TACAAATCAAATGGCTCAAATCGGCCCAAA
1 TACATATCAAATGGCCCAAATCGGCCCAAA
*
1867 TACATATCAAATGGCCTAAATCGGCCCAAA
1 TACATATCAAATGGCCCAAATCGGCCCAAA
* * *
1897 TACATA-CAAAATGGCCCAAGTCAGCCTAAA
1 TACATATC-AAATGGCCCAAATCGGCCCAAA
1927 TAC
1 TAC
1930 CCTAAGCCTA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 1 0.02
30 54 0.98
ACGTcount: A:0.42, C:0.27, G:0.13, T:0.18
Consensus pattern (30 bp):
TACATATCAAATGGCCCAAATCGGCCCAAA
Found at i:2565 original size:21 final size:21
Alignment explanation
Indices: 2531--2575 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2521 CCTTTTAAGT
* *
2531 TAATATTTATTAATTAATTAA
1 TAATAATTAATAATTAATTAA
2552 TAATAATTAATAATTAATTAA
1 TAATAATTAATAATTAATTAA
2573 TAA
1 TAA
2576 ATAAAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATAATTAATAATTAATTAA
Found at i:9255 original size:18 final size:18
Alignment explanation
Indices: 9216--9265 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
9206 TGCTTGATAT
9216 TGAAATGGCAAA-G-GATG
1 TGAAATGG-AAATGAGATG
*
9233 AGAAATGGAAATGAGATG
1 TGAAATGGAAATGAGATG
9251 TGAAATGGAATATGA
1 TGAAATGGAA-ATGA
9266 AATGGTAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 3 0.11
17 8 0.29
18 13 0.46
19 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.32, T:0.20
Consensus pattern (18 bp):
TGAAATGGAAATGAGATG
Found at i:9464 original size:24 final size:23
Alignment explanation
Indices: 9437--9481 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
9427 GAATGATGAA
* *
9437 ATTTATATAACATTACTTATTTGC
1 ATTTATACAAC-TTAATTATTTGC
*
9461 ATTTTTACAACTTAATTATTT
1 ATTTATACAACTTAATTATTT
9482 ATATCAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTATACAACTTAATTATTTGC
Found at i:10801 original size:20 final size:22
Alignment explanation
Indices: 10773--10817 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
10763 TTAATCTATT
10773 AAAAAATTA-TATAA-AC-ATA
1 AAAAAATTATTATAACACAATA
10792 AAAAACATTATTATAACACAATA
1 AAAAA-ATTATTATAACACAATA
10815 AAA
1 AAA
10818 TGCTATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.23
20 4 0.18
21 5 0.23
22 2 0.09
23 6 0.27
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAAAATTATTATAACACAATA
Found at i:16328 original size:18 final size:18
Alignment explanation
Indices: 16307--16341 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16297 AAATTATTAT
*
16307 AATTTTTAAAATTTTCAA
1 AATTCTTAAAATTTTCAA
*
16325 AATTCTTATAATTTTCA
1 AATTCTTAAAATTTTCA
16342 CAAAATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTCTTAAAATTTTCAA
Found at i:17179 original size:20 final size:20
Alignment explanation
Indices: 17130--17185 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
17120 AACCCATCAC
17130 AAGCCC-AATACCTAAA--A
1 AAGCCCAAATACCTAAACCA
* * *
17147 AAACCCAATTACCTAAACCT
1 AAGCCCAAATACCTAAACCA
*
17167 AAGCCCAAATACCAAAACC
1 AAGCCCAAATACCTAAACC
17186 CCATTACTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 5 0.17
18 9 0.30
20 16 0.53
ACGTcount: A:0.50, C:0.34, G:0.04, T:0.12
Consensus pattern (20 bp):
AAGCCCAAATACCTAAACCA
Found at i:19654 original size:219 final size:219
Alignment explanation
Indices: 19275--19696 Score: 763
Period size: 219 Copynumber: 1.9 Consensus size: 219
19265 AGGTTTAAAT
* *
19275 AATTTAATTTGTAATTCCCTATCCAGCCTAGAAGATATTACCGAATTTAAAATGTCACAATCGCA
1 AATTTAATTTGTAATCCCCTACCCAGCCTAGAAGATATTACCGAATTTAAAATGTCACAATCGCA
19340 ATTTCACCCTAAAAAACCATTTAAAACAGTTATATAATTTAATTTTGTAAATAAATTAAGACATA
66 ATTTCACCCTAAAAAACCATTTAAAACAGTTATATAATTTAATTTTGTAAATAAATTAAGACATA
*
19405 GTAAAAAAGTTAATTCCACACATTTCTGAATAACTTCAAACTTACAAATTATCAATCAAATGCCT
131 GGAAAAAAGTTAATTCCACACATTTCTGAATAACTTCAAACTTACAAATTATCAATCAAATGCCT
19470 TATACAAAAAAAGTTAATTTTTTA
196 TATACAAAAAAAGTTAATTTTTTA
* *
19494 AATTTAATTTGTAATCCCCTACCCAGCCTAGAAGATATTACCGAATTTAGAATGTCACTATCGCA
1 AATTTAATTTGTAATCCCCTACCCAGCCTAGAAGATATTACCGAATTTAAAATGTCACAATCGCA
* *
19559 ATTTCACCCTCAAAAACCATTTAAAACAGTTATATAATTTAATTTTGTAAATGAATTAAGACATA
66 ATTTCACCCTAAAAAACCATTTAAAACAGTTATATAATTTAATTTTGTAAATAAATTAAGACATA
*
19624 GGAAAAAAGTTAATTCCCCACATTTCTGAATAACTTCAAACTTACAAATTATCAATCAAATGCCT
131 GGAAAAAAGTTAATTCCACACATTTCTGAATAACTTCAAACTTACAAATTATCAATCAAATGCCT
*
19689 TATGCAAA
196 TATACAAA
19697 TATCCAAAAT
Statistics
Matches: 194, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
219 194 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.33
Consensus pattern (219 bp):
AATTTAATTTGTAATCCCCTACCCAGCCTAGAAGATATTACCGAATTTAAAATGTCACAATCGCA
ATTTCACCCTAAAAAACCATTTAAAACAGTTATATAATTTAATTTTGTAAATAAATTAAGACATA
GGAAAAAAGTTAATTCCACACATTTCTGAATAACTTCAAACTTACAAATTATCAATCAAATGCCT
TATACAAAAAAAGTTAATTTTTTA
Done.