Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013866.1 Kokia drynarioides strain JFW-HI SEQ_128894, 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: 11741
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--52 Score: 50
Period size: 3 Copynumber: 16.0 Consensus size: 3
* *
1 TAT TAT TAT TAT TAT TAAT GAGG TAGT TAT TACT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT T-AT TA-T TA-T TAT TA-T TAT TAT TAT TAT TAT
50 TAT
1 TAT
53 ACTACTTATG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
3 33 0.79
4 9 0.21
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:882 original size:3 final size:3
Alignment explanation
Indices: 868--915 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
858 AATTGGGCTC
*
868 CAA CAA CTA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
916 TAATAATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.33, G:0.00, T:0.02
Consensus pattern (3 bp):
CAA
Found at i:991 original size:15 final size:15
Alignment explanation
Indices: 973--1001 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
963 TTATTATTAT
973 TTTTTAAAATATTTA
1 TTTTTAAAATATTTA
988 TTTTTAAAATATTT
1 TTTTTAAAATATTT
1002 CTTTGAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTAAAATATTTA
Found at i:1968 original size:30 final size:31
Alignment explanation
Indices: 1934--2000 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
1924 TGTTTTAGTT
*
1934 AAATTTGATCATCAATC-TTTG-AAAAGAGTC
1 AAATTTGACCATCAA-CATTTGAAAAAGAGTC
*
1964 AAATTTGACCATTAACATTTTGAAAAAGAGTC
1 AAATTTGACCATCAACA-TTTGAAAAAGAGTC
1996 AAATT
1 AAATT
2001 GATATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 1 0.03
30 13 0.41
31 4 0.12
32 14 0.44
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (31 bp):
AAATTTGACCATCAACATTTGAAAAAGAGTC
Found at i:5659 original size:15 final size:15
Alignment explanation
Indices: 5641--5692 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
5631 ATCCAATATT
5641 AATATTTTAATAATA
1 AATATTTTAATAATA
*
5656 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
5675 AATATATTAATAATA
1 AATATTTTAATAATA
5690 AAT
1 AAT
5693 GTCTTGTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 13 0.43
16 2 0.07
17 4 0.13
18 1 0.03
19 10 0.33
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:11393 original size:29 final size:28
Alignment explanation
Indices: 11341--11581 Score: 136
Period size: 30 Copynumber: 8.2 Consensus size: 28
11331 TATTTTGGGT
*
11341 GAAA-TTCGA-GGTAAAAATGGAATTTTG
1 GAAAGTTCGAGGGT-AAAATGTAATTTTG
*
11368 GAAAGTTCGGGGGTAAAATGGTAATTTTTCG
1 GAAAGTTCGAGGGTAAAAT-GTAA-TTTT-G
** *
11399 TGAAA--TCGAGATTAAAAATGAAATTTTG
1 -GAAAGTTCGAGGGT-AAAATGTAATTTTG
*
11427 GAAAATTCGAGGGTAAAATTGTAATTTTG
1 GAAAGTTCGAGGGTAAAA-TGTAATTTTG
*
11456 GAAAGTAT--AGGAGTAAAATGTCAATTTTA
1 GAAAGT-TCGAGG-GTAAAATGT-AATTTTG
* *
11485 GAATGTTCGAGGGTAAAAATGTAATTTTTAA
1 GAAAGTTCGAGGGT-AAAATGTAA-TTTT-G
* * *
11516 GAAA-TTCAAGGATAAAAATGTAATTTTTA
1 GAAAGTTCGAGGGT-AAAATGTAA-TTTTG
* * *
11545 GAAAGTTCGGGGGTTAAAGTATAATTATTG
1 GAAAGTTCGAGGG-TAAAATGTAATT-TTG
*
11575 GATAGTT
1 GAAAGTT
11582 TAGGGACCTT
Statistics
Matches: 171, Mismatches: 22, Indels: 39
0.74 0.09 0.17
Matches are distributed among these distances:
27 8 0.05
28 21 0.12
29 58 0.34
30 69 0.40
31 11 0.06
32 4 0.02
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (28 bp):
GAAAGTTCGAGGGTAAAATGTAATTTTG
Found at i:11415 original size:59 final size:59
Alignment explanation
Indices: 11339--11454 Score: 171
Period size: 59 Copynumber: 2.0 Consensus size: 59
11329 GATATTTTGG
* * *
11339 GTGAAATTCGAGGTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTC
1 GTGAAATTCGAGGTAAAAATGAAATTTTGGAAAATTCGAGGGTAAAATGGTAATTTTTC
* *
11398 GTGAAA-TCGAGATTAAAAATGAAATTTTGGAAAATTCGAGGGTAAAATTGTAATTTT
1 GTGAAATTCGAG-GTAAAAATGAAATTTTGGAAAATTCGAGGGTAAAATGGTAATTTT
11455 GGAAAGTATA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 5 0.10
59 46 0.90
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (59 bp):
GTGAAATTCGAGGTAAAAATGAAATTTTGGAAAATTCGAGGGTAAAATGGTAATTTTTC
Found at i:11506 original size:30 final size:30
Alignment explanation
Indices: 11341--11558 Score: 147
Period size: 29 Copynumber: 7.5 Consensus size: 30
11331 TATTTTGGGT
* *
11341 GAAA-TTCGA-GGTAAAAATGGAA-TTTTG
1 GAAAGTTCGAGGGTAAAAATGTAATTTTTA
* *
11368 GAAAGTTCGGGGGT-AAAATGGTAATTTTTCGT
1 GAAAGTTCGAGGGTAAAAAT-GTAATTTTT--A
** * *
11400 GAAA--TCGAGATTAAAAATG-AAATTTTG
1 GAAAGTTCGAGGGTAAAAATGTAATTTTTA
* * *
11427 GAAAATTCGAGGGTAAAATTGTAA-TTTTG
1 GAAAGTTCGAGGGTAAAAATGTAATTTTTA
11456 GAAAGTAT--AGGAGT-AAAATGTCAA-TTTTA
1 GAAAGT-TCGAGG-GTAAAAATGT-AATTTTTA
*
11485 GAATGTTCGAGGGTAAAAATGTAATTTTTAA
1 GAAAGTTCGAGGGTAAAAATGTAATTTTT-A
* *
11516 GAAA-TTCAAGGATAAAAATGTAATTTTTA
1 GAAAGTTCGAGGGTAAAAATGTAATTTTTA
*
11545 GAAAGTTCGGGGGT
1 GAAAGTTCGAGGGT
11559 TAAAGTATAA
Statistics
Matches: 151, Mismatches: 21, Indels: 35
0.73 0.10 0.17
Matches are distributed among these distances:
27 8 0.05
28 19 0.13
29 56 0.37
30 55 0.36
31 9 0.06
32 4 0.03
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (30 bp):
GAAAGTTCGAGGGTAAAAATGTAATTTTTA
Done.