Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003695.1 Kokia drynarioides strain JFW-HI SEQ_116628, 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: 33148
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:4497 original size:21 final size:19
Alignment explanation
Indices: 4473--4514 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
4463 TAGTTTTTAA
*
4473 TGTAACTATGTTAATTTAGTT
1 TGTAACT-TGTTAACTTA-TT
4494 TGTAACTTGTTAACTTATT
1 TGTAACTTGTTAACTTATT
4513 TG
1 TG
4515 GTTATGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.52
Consensus pattern (19 bp):
TGTAACTTGTTAACTTATT
Found at i:9001 original size:21 final size:19
Alignment explanation
Indices: 8977--9018 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
8967 TAGTTTTTAA
*
8977 TGTAACTATGTTAATTTAGTT
1 TGTAACT-TGTTAACTTA-TT
8998 TGTAACTTGTTAACTTATT
1 TGTAACTTGTTAACTTATT
9017 TG
1 TG
9019 GTTATGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.52
Consensus pattern (19 bp):
TGTAACTTGTTAACTTATT
Found at i:32262 original size:28 final size:28
Alignment explanation
Indices: 32201--32255 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
32191 TATTATAAAA
32201 AAATTATTAATAATCAAAATGATATATC
1 AAATTATTAATAATCAAAATGATATATC
* * *
32229 AAATTATTATTTATCAAAATGGTATAT
1 AAATTATTAATAATCAAAATGATATAT
32256 TTAATTAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (28 bp):
AAATTATTAATAATCAAAATGATATATC
Found at i:32668 original size:4 final size:4
Alignment explanation
Indices: 32661--32694 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
32651 AAATTGAAGG
*
32661 AAGA AAGA AAGA AAAA AGAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA A-AGA AAGA AAGA AAGA A
32695 GGAATAAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 24 0.89
5 3 0.11
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:32690 original size:25 final size:25
Alignment explanation
Indices: 32661--32708 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
32651 AAATTGAAGG
32661 AAGAAAGAAAGAAAAAAGAGAAAGA
1 AAGAAAGAAAGAAAAAAGAGAAAGA
* * *
32686 AAGAAAGAAGGAATAAGGAGAAA
1 AAGAAAGAAAGAAAAAAGAGAAA
32709 AAGGGAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (25 bp):
AAGAAAGAAAGAAAAAAGAGAAAGA
Found at i:32735 original size:25 final size:25
Alignment explanation
Indices: 32688--32734 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
32678 GAGAAAGAAA
* *
32688 GAAAGAAGGAATAAGGAGAAAAAGG
1 GAAAGAAGGAAGAAGGAAAAAAAGG
32713 GAAAGAAGG-AGAAGGAAAAAAA
1 GAAAGAAGGAAGAAGGAAAAAAA
32735 AAAAGATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (25 bp):
GAAAGAAGGAAGAAGGAAAAAAAGG
Found at i:32951 original size:12 final size:12
Alignment explanation
Indices: 32934--33017 Score: 50
Period size: 12 Copynumber: 6.9 Consensus size: 12
32924 TTAAAATATT
32934 TTAATTTGTTAA
1 TTAATTTGTTAA
*
32946 TTAATTTGATTATT
1 TTAATTTG-TTA-A
*
32960 TTAAGTTT-TTTA
1 TTAA-TTTGTTAA
*
32972 TT--TTTTTTAA
1 TTAATTTGTTAA
32982 TTTAATTT-TTAA
1 -TTAATTTGTTAA
* *
32994 TTGATTTGTTAT
1 TTAATTTGTTAA
33006 TTAATATTGTTA
1 TTAAT-TTGTTA
33018 TAGTTGAGTA
Statistics
Matches: 56, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
9 3 0.05
10 3 0.05
11 8 0.14
12 21 0.38
13 14 0.25
14 4 0.07
15 3 0.05
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.65
Consensus pattern (12 bp):
TTAATTTGTTAA
Found at i:33007 original size:23 final size:22
Alignment explanation
Indices: 32933--33010 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 22
32923 TTTAAAATAT
32933 TTTAATTTGTTAATTAATTTGATTA
1 TTTAATTT-TTAATT-ATTTG-TTA
* *
32958 TTTTAAGTTTTTTATT-TTTTTTAA
1 -TTTAA-TTTTTAATTATTTGTT-A
32982 TTTAATTTTTAATTGATTTGTTA
1 TTTAATTTTTAATT-ATTTGTTA
33005 TTTAAT
1 TTTAAT
33011 ATTGTTATAG
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
22 8 0.18
23 14 0.32
24 9 0.20
26 10 0.23
27 3 0.07
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (22 bp):
TTTAATTTTTAATTATTTGTTA
Found at i:33126 original size:20 final size:21
Alignment explanation
Indices: 33085--33127 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
33075 TAATTTACTT
33085 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
33106 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
33126 TA
1 TA
33128 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Done.