Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003299.1 Kokia drynarioides strain JFW-HI SEQ_115978, 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: 21947
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Found at i:8672 original size:24 final size:24
Alignment explanation
Indices: 8623--8673 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
8613 AATTCTAGTC
* *
8623 AATGCAAAATATATTTTGCTAATA
1 AATGCAAAATATATTATACTAATA
* *
8647 AATGCTAAATATATTATACTACTA
1 AATGCAAAATATATTATACTAATA
8671 AAT
1 AAT
8674 CTTTTAGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (24 bp):
AATGCAAAATATATTATACTAATA
Found at i:11000 original size:24 final size:24
Alignment explanation
Indices: 10973--11019 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
10963 AAGCCTAATT
* *
10973 CTAATCAATTCAAAATATATTATG
1 CTAATAAATGCAAAATATATTATG
*
10997 CTAATAAATGCTAAATATATTAT
1 CTAATAAATGCAAAATATATTAT
11020 ACTACTAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (24 bp):
CTAATAAATGCAAAATATATTATG
Found at i:11242 original size:12 final size:12
Alignment explanation
Indices: 11227--11252 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11217 ATAAATTAAA
11227 ATTTAAAAATAT
1 ATTTAAAAATAT
11239 ATTTAAAAATAT
1 ATTTAAAAATAT
11251 AT
1 AT
11253 AAATTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTTAAAAATAT
Found at i:13181 original size:26 final size:26
Alignment explanation
Indices: 13151--13212 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
13141 AATTTATTTC
*
13151 TTTTATATATTTATAGTTTCTTATA-A
1 TTTTATATAATTATAG-TTCTTATATA
* *
13177 TTTTATAAAATTATAGTTCTTTTATA
1 TTTTATATAATTATAGTTCTTATATA
13203 TATTTATATA
1 T-TTTATATA
13213 CTTTTATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 7 0.23
26 16 0.53
27 7 0.23
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (26 bp):
TTTTATATAATTATAGTTCTTATATA
Found at i:13201 original size:19 final size:18
Alignment explanation
Indices: 13172--13222 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
13162 TATAGTTTCT
*
13172 TATAATTTTATAAAATTA
1 TATACTTTTATAAAATTA
* * *
13190 TAGTTCTTTTATATATTTA
1 TA-TACTTTTATAAAATTA
13209 TATACTTTTATAAA
1 TATACTTTTATAAA
13223 TTTACAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (18 bp):
TATACTTTTATAAAATTA
Found at i:13218 original size:18 final size:18
Alignment explanation
Indices: 13172--13226 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
13162 TATAGTTTCT
* *
13172 TATAATTTTATAAAATTA
1 TATACTTTTATAAATTTA
* *
13190 TAGTTCTTTTATATATTTA
1 TA-TACTTTTATAAATTTA
13209 TATACTTTTATAAATTTA
1 TATACTTTTATAAATTTA
13227 CAAAATTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (18 bp):
TATACTTTTATAAATTTA
Found at i:13220 original size:45 final size:45
Alignment explanation
Indices: 13148--13233 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 45
13138 ACCAATTTAT
* *
13148 TTCTTTTATATATTTATAGTTTCTTATAATTTTATAAAATTATAG
1 TTCTTTTATATATTTATAGTTTCTTATAAATTTACAAAATTATAG
13193 TTCTTTTATATATTTATA-TACTT-TTATAAATTTACAAAATT
1 TTCTTTTATATATTTATAGT--TTCTTATAAATTTACAAAATT
13234 TTAAACTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
44 1 0.03
45 34 0.92
46 2 0.05
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (45 bp):
TTCTTTTATATATTTATAGTTTCTTATAAATTTACAAAATTATAG
Found at i:13549 original size:19 final size:21
Alignment explanation
Indices: 13510--13550 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
13500 TAAAAAAAAC
*
13510 TATATACTTTTTAAATTAATT
1 TATATACTTTTTAAATGAATT
13531 TATATA-TTTTTAAA-GAATT
1 TATATACTTTTTAAATGAATT
13550 T
1 T
13551 TTAATCTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 8 0.42
21 6 0.32
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TATATACTTTTTAAATGAATT
Found at i:13690 original size:32 final size:33
Alignment explanation
Indices: 13654--13750 Score: 101
Period size: 32 Copynumber: 3.0 Consensus size: 33
13644 TAGTGATGAG
13654 GTACCAAAC-TGAGTGACGCAATACAAGTTAAT
1 GTACCAAACTTGAGTGACGCAATACAAGTTAAT
* * *
13686 GTACC-AACTTGGGTGATGGAATACAAGTTAAT
1 GTACCAAACTTGAGTGACGCAATACAAGTTAAT
* * * * *
13718 GTACC-ACCTTGGGTGAGGGAATAAAAGTTAAT
1 GTACCAAACTTGAGTGACGCAATACAAGTTAAT
13750 G
1 G
13751 GAGAGTTACT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 3 0.05
32 55 0.95
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (33 bp):
GTACCAAACTTGAGTGACGCAATACAAGTTAAT
Found at i:15586 original size:19 final size:18
Alignment explanation
Indices: 15548--15592 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
15538 GAATTTAAGG
* *
15548 GAGAATTGAGAGATATTT
1 GAGAATTGAGAGAGAGTT
15566 GAGAATGTGAGAGAGAGTT
1 GAGAAT-TGAGAGAGAGTT
15585 GAG-ATTGA
1 GAGAATTGA
15593 ATTGCAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 8 0.33
19 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.36, T:0.27
Consensus pattern (18 bp):
GAGAATTGAGAGAGAGTT
Found at i:20502 original size:44 final size:44
Alignment explanation
Indices: 20403--20542 Score: 174
Period size: 44 Copynumber: 3.0 Consensus size: 44
20393 TAGTTGTGAA
* *
20403 TTTATTTCTTTTATATATTTATACATATTATTTTATAAATTTAT-TAAT
1 TTTAGTTCTTTTATATA-TT-T--ATATT-TTTTATAAATTTATAAAAT
*
20451 TTGTAGTTCTTTTATATATTTATATTTTTTATAAACTTATAAAAT
1 TT-TAGTTCTTTTATATATTTATATTTTTTATAAATTTATAAAAT
*
20496 TTTAGTTCTTTTATATATTTATATATATTTATAAATTTATAAAAT
1 TTTAGTTCTTTTATATATTTATAT-TTTTTATAAATTTATAAAAT
20541 TT
1 TT
20543 AAATTTTTAT
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
44 35 0.42
45 30 0.36
47 1 0.01
48 4 0.05
49 14 0.17
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (44 bp):
TTTAGTTCTTTTATATATTTATATTTTTTATAAATTTATAAAAT
Found at i:20622 original size:20 final size:20
Alignment explanation
Indices: 20599--20645 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
20589 ACTTTTCAAA
20599 ATATTTGAAGTTTTTTTTAT
1 ATATTTGAAGTTTTTTTTAT
* *
20619 ATATTTTTAATTTTTTTTTAT
1 ATA-TTTGAAGTTTTTTTTAT
*
20640 AAATTT
1 ATATTT
20646 ATATTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (20 bp):
ATATTTGAAGTTTTTTTTAT
Found at i:20646 original size:19 final size:21
Alignment explanation
Indices: 20609--20652 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
20599 ATATTTGAAG
**
20609 TTTTTTTTATATATTTTTA-A
1 TTTTTTTTATATAAATTTATA
20629 TTTTTTTT-TATAAATTTATA
1 TTTTTTTTATATAAATTTATA
20649 TTTT
1 TTTT
20653 ATATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTTTTATATAAATTTATA
Done.