Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013579.1 Kokia drynarioides strain JFW-HI SEQ_128605, 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: 69718
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:133 original size:16 final size:17
Alignment explanation
Indices: 96--133 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
86 AATTTATAAT
96 ATTT-TATATTATGTTA
1 ATTTATATATTATGTTA
112 ACTTTATATATTATG-TA
1 A-TTTATATATTATGTTA
129 ATTTA
1 ATTTA
134 AAACACATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (17 bp):
ATTTATATATTATGTTA
Found at i:9590 original size:123 final size:123
Alignment explanation
Indices: 9428--9676 Score: 462
Period size: 123 Copynumber: 2.0 Consensus size: 123
9418 CCATCAAACA
*
9428 ATACCAAATAAAGAGGACCAATCCACATCCTAAAAGACTAAATCAAATTTATTCCTCAAATTAGC
1 ATACCAAATAAAGACGACCAATCCACATCCTAAAAGACTAAATCAAATTTATTCCTCAAATTAGC
9493 AAAAAGCCAATCCTCCAACTAATAATAGAAAATTCGAGACAATAGCCTCGACGGAATG
66 AAAAAGCCAATCCTCCAACTAATAATAGAAAATTCGAGACAATAGCCTCGACGGAATG
*
9551 ATACCAAATAAAGACGACCAATCCACATCCTGAAAGACTAAATCAAATTTATTCCTCAAATTAGC
1 ATACCAAATAAAGACGACCAATCCACATCCTAAAAGACTAAATCAAATTTATTCCTCAAATTAGC
* *
9616 AAAAAGTCAATCCTCCAACTAATAATAGAAAATTCGAGACAATAGCCTCGATGGAATG
66 AAAAAGCCAATCCTCCAACTAATAATAGAAAATTCGAGACAATAGCCTCGACGGAATG
9674 ATA
1 ATA
9677 TGCTCCCACA
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 122 1.00
ACGTcount: A:0.45, C:0.22, G:0.11, T:0.21
Consensus pattern (123 bp):
ATACCAAATAAAGACGACCAATCCACATCCTAAAAGACTAAATCAAATTTATTCCTCAAATTAGC
AAAAAGCCAATCCTCCAACTAATAATAGAAAATTCGAGACAATAGCCTCGACGGAATG
Found at i:13245 original size:23 final size:23
Alignment explanation
Indices: 13219--13270 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
13209 TTTATCGTTT
*
13219 GTTTATTATTCATAAACATGTTC
1 GTTTAATATTCATAAACATGTTC
* * *
13242 GTTTAATGTTCGTGAACATGTTC
1 GTTTAATATTCATAAACATGTTC
*
13265 GGTTAA
1 GTTTAA
13271 GTTAAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (23 bp):
GTTTAATATTCATAAACATGTTC
Found at i:16418 original size:22 final size:22
Alignment explanation
Indices: 16382--16423 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16372 CCTCAAACCC
* *
16382 AAACCTTAAATCTTGAATCTTA
1 AAACCTCAAACCTTGAATCTTA
16404 AAACCTCAAACCTTGAATCT
1 AAACCTCAAACCTTGAATCT
16424 CGAACCCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.31
Consensus pattern (22 bp):
AAACCTCAAACCTTGAATCTTA
Found at i:20074 original size:31 final size:30
Alignment explanation
Indices: 20011--20088 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
20001 AATAGTTTAT
*
20011 ATTTTTATAATTTTTAAAATATTAAATTAA
1 ATTTTTATAATTTTTAAAAGATTAAATTAA
*
20041 ATTTTTATTAA-TTTTAAAAGATTAATTTAA
1 ATTTTTA-TAATTTTTAAAAGATTAAATTAA
* * *
20071 AATTTTAAAAATTTTAAA
1 ATTTTTATAATTTTTAAA
20089 TGAAAAATCC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 2 0.05
30 37 0.88
31 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
ATTTTTATAATTTTTAAAAGATTAAATTAA
Found at i:26393 original size:18 final size:18
Alignment explanation
Indices: 26370--26414 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
26360 TAATTTTATA
26370 TGGATTCTATTTTACCAT
1 TGGATTCTATTTTACCAT
* **
26388 TGGATTCTGTTTTTTCAT
1 TGGATTCTATTTTACCAT
26406 TGGATTCTA
1 TGGATTCTA
26415 AATTTCCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.53
Consensus pattern (18 bp):
TGGATTCTATTTTACCAT
Found at i:45127 original size:3 final size:3
Alignment explanation
Indices: 45119--45159 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
45109 TTTTTAACTG
** *
45119 TTA TTA TTA TTA CAA TTA TTA TTA TTA TCA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
45160 CAACCTTTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:45139 original size:15 final size:15
Alignment explanation
Indices: 45119--45159 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
45109 TTTTTAACTG
45119 TTATTATTATTA-CAA
1 TTATTATTATTATC-A
45134 TTATTATTATTATCA
1 TTATTATTATTATCA
45149 TTATTATTATT
1 TTATTATTATT
45160 CAACCTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 24 0.96
16 1 0.04
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATTATTATTATCA
Found at i:45545 original size:32 final size:32
Alignment explanation
Indices: 45483--45545 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
45473 GATAGCGCTA
*
45483 CAATTAAAGAAGGTAGAAATTTAAAAGTTAAT
1 CAATTAAAGAAGGTACAAATTTAAAAGTTAAT
45515 CAATTAAA-AA-GTACAAATTTATAAATGTTAA
1 CAATTAAAGAAGGTACAAATTTA-AAA-GTTAA
45546 CAAACCATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 10 0.36
31 5 0.18
32 13 0.46
ACGTcount: A:0.54, C:0.05, G:0.11, T:0.30
Consensus pattern (32 bp):
CAATTAAAGAAGGTACAAATTTAAAAGTTAAT
Found at i:49995 original size:26 final size:28
Alignment explanation
Indices: 49944--49995 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
49934 TTGTATTGTT
*
49944 TTTATTTAATAATTTTATATATTTTTCA
1 TTTATTTAATAATTTTATATAGTTTTCA
49972 TTTA-TTAA-AATTTTATATAGTTTT
1 TTTATTTAATAATTTTATATAGTTTT
49996 ATGTGTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 15 0.65
27 4 0.17
28 4 0.17
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTATTTAATAATTTTATATAGTTTTCA
Found at i:50005 original size:26 final size:25
Alignment explanation
Indices: 49948--50008 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 25
49938 ATTGTTTTTA
*
49948 TTTAATAATTTTATATATTTTTCATT
1 TTTAA-AATTTTATATAGTTTTCATT
49974 TATTAAAATTTTATATAGTTTT-ATGT
1 T-TTAAAATTTTATATAGTTTTCAT-T
50000 GTTTAAAAT
1 -TTTAAAAT
50009 ATAATATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
25 2 0.06
26 24 0.77
27 5 0.16
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (25 bp):
TTTAAAATTTTATATAGTTTTCATT
Found at i:50739 original size:20 final size:21
Alignment explanation
Indices: 50699--50739 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
50689 GAGTGTTTCT
50699 AATTGTTATATTAATAACAAA
1 AATTGTTATATTAATAACAAA
50720 AATTGTT-TATATAA-AACAAA
1 AATTGTTATAT-TAATAACAAA
50740 TGAATGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (21 bp):
AATTGTTATATTAATAACAAA
Found at i:69609 original size:21 final size:21
Alignment explanation
Indices: 69553--69612 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
69543 AACGGGCATT
*
69553 GAAAGAAAAGAAAG-AAGGAA
1 GAAAGAGAAGAAAGAAAGGAA
69573 GAAAGAGAAGAAAGAAAGG-A
1 GAAAGAGAAGAAAGAAAGGAA
* *
69593 GAAGGAGAATGAGAGAAAGG
1 GAAAGAGAA-GAAAGAAAGG
69613 TAATGTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.62, C:0.00, G:0.37, T:0.02
Consensus pattern (21 bp):
GAAAGAGAAGAAAGAAAGGAA
Done.