Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000810.1 Kokia drynarioides strain JFW-HI SEQ_111890, 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: 28259
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 14 characters in sequence are not A, C, G, or T
Found at i:752 original size:17 final size:17
Alignment explanation
Indices: 725--757 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
715 ATAACGGGAA
725 ATTTTTTAAT-ATTTTG
1 ATTTTTTAATAATTTTG
741 ATTTTTTAAATAATTTT
1 ATTTTTT-AATAATTTT
758 AAAATTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
ATTTTTTAATAATTTTG
Found at i:5382 original size:55 final size:55
Alignment explanation
Indices: 5316--5584 Score: 238
Period size: 55 Copynumber: 4.8 Consensus size: 55
5306 TACATAATAA
5316 TCGATTTAAACATATAAACAATCAATTCAAAAAAAATAATATTCCAATATAACAG
1 TCGATTTAAACATATAAACAATCAATTCAAAAAAAATAATATTCCAATATAACAG
* * *
5371 TCGATTTAAACATATAAACAAACGATTCAAAAGAAGAAAAAACAATATTCC-ATCATAACAG
1 TCGATTTAAACATATAAACAATCAATTC-----AA-AAAAAATAATATTCCAAT-ATAACAG
* * * **
5432 TCTATTTAAACATATAAACAATCAATTCAAAAGAAGTAATATTCCACCATAAC-G
1 TCGATTTAAACATATAAACAATCAATTCAAAAAAAATAATATTCCAATATAACAG
* ** * * * * * * *
5486 ATTGATTTAAATGTATAAACAATAAATTCAAAAGAAACAGTATTTCAATATGACAA
1 -TCGATTTAAACATATAAACAATCAATTCAAAAAAAATAATATTCCAATATAACAG
* * * *
5542 TCAATTTAGACATAAAAAATAATCAATT-AAAAAAAATAATATT
1 TCGATTTAAACAT-ATAAACAATCAATTCAAAAAAAATAATATT
5585 TTTGAGAAAT
Statistics
Matches: 168, Mismatches: 35, Indels: 22
0.75 0.16 0.10
Matches are distributed among these distances:
54 1 0.01
55 104 0.62
56 13 0.08
60 4 0.02
61 46 0.27
ACGTcount: A:0.54, C:0.13, G:0.06, T:0.27
Consensus pattern (55 bp):
TCGATTTAAACATATAAACAATCAATTCAAAAAAAATAATATTCCAATATAACAG
Found at i:5419 original size:61 final size:61
Alignment explanation
Indices: 5316--5467 Score: 210
Period size: 61 Copynumber: 2.6 Consensus size: 61
5306 TACATAATAA
*
5316 TCGATTTAAACATATAAACAATCAATTC-----AA-AAAAAATAATATTCCAAT-ATAACAG
1 TCGATTTAAACATATAAACAATCAATTCAAAAGAAGAAAAAACAATATTCC-ATCATAACAG
* *
5371 TCGATTTAAACATATAAACAAACGATTCAAAAGAAGAAAAAACAATATTCCATCATAACAG
1 TCGATTTAAACATATAAACAATCAATTCAAAAGAAGAAAAAACAATATTCCATCATAACAG
*
5432 TCTATTTAAACATATAAACAATCAATTCAAAAGAAG
1 TCGATTTAAACATATAAACAATCAATTCAAAAGAAG
5468 TAATATTCCA
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
55 26 0.31
60 4 0.05
61 54 0.64
ACGTcount: A:0.54, C:0.15, G:0.06, T:0.25
Consensus pattern (61 bp):
TCGATTTAAACATATAAACAATCAATTCAAAAGAAGAAAAAACAATATTCCATCATAACAG
Found at i:21198 original size:26 final size:25
Alignment explanation
Indices: 21147--21198 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
21137 CAAGTTATTG
* *
21147 ATTTGATTTAATTACATTATATTTT
1 ATTTGATTTAATTACATAATAATTT
*
21172 ATTTTATTTATATTACATAATAATTT
1 ATTTGATTTA-ATTACATAATAATTT
21198 A
1 A
21199 ATTAAATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTTGATTTAATTACATAATAATTT
Found at i:25808 original size:32 final size:32
Alignment explanation
Indices: 25747--25811 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
25737 TTAGTTTCAA
*
25747 ATAATATATTTTATTATTTATTATATGTTATT
1 ATAATATATTTGATTATTTATTATATGTTATT
*
25779 ATAATATCATTTGA-TA-TTATTCATTTGTTATT
1 ATAATAT-ATTTGATTATTTATT-ATATGTTATT
25811 A
1 A
25812 AAAAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 5 0.17
32 19 0.66
33 5 0.17
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (32 bp):
ATAATATATTTGATTATTTATTATATGTTATT
Found at i:28106 original size:4 final size:4
Alignment explanation
Indices: 28097--28147 Score: 57
Period size: 4 Copynumber: 12.2 Consensus size: 4
28087 AAATAAACGG
* * *
28097 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAT GAGA GAAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA GAAA
28147 G
1 G
28148 GTAATGTGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 32 0.82
5 7 0.18
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:28119 original size:17 final size:17
Alignment explanation
Indices: 28097--28147 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
28087 AAATAAACGG
28097 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
28114 GAAAGAAAGAAAGG-AA
1 GAAAGAAAGAAAGGAAA
* * *
28130 GAATGAGAGAAAAGAAA
1 GAAAGAAAGAAAGGAAA
28147 G
1 G
28148 GTAATGTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 13 0.43
17 17 0.57
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Done.