Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003094.1 Kokia drynarioides strain JFW-HI SEQ_115655, 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: 2699
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Found at i:781 original size:29 final size:29
Alignment explanation
Indices: 747--962 Score: 126
Period size: 29 Copynumber: 7.3 Consensus size: 29
737 CGAAAAACGA
*
747 AATTTTTGGACATCCGGGGTTAAAATGGT
1 AATTTTTGGACATTCGGGGTTAAAATGGT
* * * * *
776 AATTTTTAGGAAAATCGAGATCAAAATGG-
1 AATTTTT-GGACATTCGGGGTTAAAATGGT
*
805 AATTTTTGGACATTCGAGGG-TAAAAGGGT
1 AATTTTTGGACATTCG-GGGTTAAAATGGT
* *
834 AATTTTT-GAAAGTTTTGGGGTTAAAAAATGG-
1 AATTTTTGGACA--TTCGGGGTT--AAAATGGT
**
865 AATTTTTGGACATAT-GGGGGCAAAATGGT
1 AATTTTTGGACAT-TCGGGGTTAAAATGGT
*
894 AATTTTTGGA-AGTTTCGAGGTTAAAAATGG-
1 AATTTTTGGACA--TTCGGGGTT-AAAATGGT
* * *
924 ATTTTTTTGGA-AGTTTGGGGTAAAAATGG-
1 A-ATTTTTGGACA-TTCGGGGTTAAAATGGT
953 AATTTTTGGA
1 AATTTTTGGA
963 AGTTTCAAGG
Statistics
Matches: 144, Mismatches: 27, Indels: 33
0.71 0.13 0.16
Matches are distributed among these distances:
28 32 0.22
29 44 0.31
30 35 0.24
31 24 0.17
32 9 0.06
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (29 bp):
AATTTTTGGACATTCGGGGTTAAAATGGT
Found at i:931 original size:60 final size:57
Alignment explanation
Indices: 747--1047 Score: 245
Period size: 58 Copynumber: 5.1 Consensus size: 57
737 CGAAAAACGA
* ** ** * *
747 AATTTTTGGACATCCGGGGTTAAAATGGTAATTTTTAGGAA-AATCGAGATCAAAATGG
1 AATTTTTGGACAT-TGGGGGAAAAATGGTAATTTTT-GGAAGTTTCGAGGTAAAAATGG
* * * * * *
805 AATTTTTGGACATTCGAGGGTAAAAGGGTAATTTTTGAAAGTTTTGGGGTTAAAAAATGG
1 AATTTTTGGACATT-GGGGGAAAAATGGTAATTTTTGGAAGTTTCGAGG-T-AAAAATGG
*
865 AATTTTTGGACATATGGGGGCAAAATGGTAATTTTTGGAAGTTTCGAGGTTAAAAATGG
1 AATTTTTGGACAT-TGGGGGAAAAATGGTAATTTTTGGAAGTTTCGAGG-TAAAAATGG
* * *
924 ATTTTTTTGGA-AGTTTGGGGTAAAAATGG-AATTTTTGGAAGTTTCAAGGTAAAGAA-GG
1 A-ATTTTTGGACA--TTGGGGGAAAAATGGTAATTTTTGGAAGTTTCGAGGTAAA-AATGG
* * *
982 AATCTTTGGA-AGTTCGGGGGTAAAAAT-ATAATTTTTGGAAGTTTCGAGGTCAAAATGG
1 AATTTTTGGACA-TT-GGGGG-AAAAATGGTAATTTTTGGAAGTTTCGAGGTAAAAATGG
*
1040 GATTTTTG
1 AATTTTTG
1048 AACAGTTAAG
Statistics
Matches: 200, Mismatches: 30, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
56 2 0.01
57 17 0.09
58 77 0.38
59 32 0.16
60 70 0.35
61 2 0.01
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.35
Consensus pattern (57 bp):
AATTTTTGGACATTGGGGGAAAAATGGTAATTTTTGGAAGTTTCGAGGTAAAAATGG
Found at i:957 original size:59 final size:57
Alignment explanation
Indices: 762--1047 Score: 231
Period size: 60 Copynumber: 4.9 Consensus size: 57
752 TTGGACATCC
* ** * * *
762 GGGGTTAAAATGGTAATTTTTAGGAA-AATCGAGATCAAAATGGAATTTTTGGACA-TTC
1 GGGGTAAAAATGG-AATTTTT-GGAAGTTTCGAGGTAAAAATGGAATTTTTGGA-AGTTT
* * * * *
820 GAGGGT-AAAAGGGTAATTTTTGAAAGTTTTGGGGTTAAAAAATGGAATTTTTGGACA-TAT
1 G-GGGTAAAAATGG-AATTTTTGGAAGTTTCGAGG-T-AAAAATGGAATTTTTGGA-AGTTT
** *
880 GGGGGCAAAATGGTAATTTTTGGAAGTTTCGAGGTTAAAAATGGATTTTTTTGGAAGTTT
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTCGAGG-TAAAAATGGA-ATTTTTGGAAGTTT
* * *
940 GGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTAAAGAA-GGAATCTTTGGAAGTTCG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTAAA-AATGGAATTTTTGGAAGTT-T
** * *
998 GGGGTAAAAATATAATTTTTGGAAGTTTCGAGGTCAAAATGGGATTTTTG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTG
1048 AACAGTTAAG
Statistics
Matches: 189, Mismatches: 29, Indels: 20
0.79 0.12 0.08
Matches are distributed among these distances:
57 16 0.08
58 66 0.35
59 39 0.21
60 68 0.36
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.34
Consensus pattern (57 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTGGAAGTTT
Found at i:974 original size:29 final size:29
Alignment explanation
Indices: 798--1047 Score: 192
Period size: 29 Copynumber: 8.5 Consensus size: 29
788 AATCGAGATC
798 AAAATGGAATTTTTGGACA--TTCGAGGGT-
1 AAAATGGAATTTTTGGA-AGTTTCGA-GGTA
* * * *
826 AAAAGGGTAATTTTTGAAAGTTTTGGGGTTAA
1 AAAATGG-AATTTTTGGAAGTTTCGAGG-T-A
* * **
858 AAAATGGAATTTTTGGACA-TAT-GGGGGC
1 AAAATGGAATTTTTGGA-AGTTTCGAGGTA
886 AAAATGGTAATTTTTGGAAGTTTCGAGGTTA
1 AAAATGG-AATTTTTGGAAGTTTCGAGG-TA
* *
917 AAAATGGATTTTTTTGGAAGTTT-GGGGTA
1 AAAATGGA-ATTTTTGGAAGTTTCGAGGTA
*
946 AAAATGGAATTTTTGGAAGTTTCAAGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTA
* *
975 AAGAA-GGAATCTTTGGAAG-TTCGGGGGTA
1 AA-AATGGAATTTTTGGAAGTTTC-GAGGTA
** *
1004 AAAATATAATTTTTGGAAGTTTCGAGGTC
1 AAAATGGAATTTTTGGAAGTTTCGAGGTA
*
1033 AAAATGGGATTTTTG
1 AAAATGGAATTTTTG
1048 AACAGTTAAG
Statistics
Matches: 176, Mismatches: 29, Indels: 33
0.74 0.12 0.14
Matches are distributed among these distances:
28 33 0.19
29 85 0.48
30 20 0.11
31 31 0.18
32 7 0.04
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGTA
Done.