Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008260.1 Kokia drynarioides strain JFW-HI SEQ_122925, 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: 38805
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:1467 original size:2 final size:2
Alignment explanation
Indices: 1460--1485 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1450 ATAACTCGTG
1460 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1486 CACATTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2224 original size:10 final size:10
Alignment explanation
Indices: 2209--2254 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
2199 TTTTATACCT
2209 TAATTAAATC
1 TAATTAAATC
2219 TAATT-AATC
1 TAATTAAATC
*
2228 TTAATT-AATT
1 -TAATTAAATC
*
2238 TAATTAAACC
1 TAATTAAATC
2248 TAATTAA
1 TAATTAA
2255 CTTAACCTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 9 0.29
10 22 0.71
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (10 bp):
TAATTAAATC
Found at i:2243 original size:19 final size:19
Alignment explanation
Indices: 2207--2259 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2197 ACTTTTATAC
* *
2207 CTTAATTAAATCTAATTAAT
1 CTTAATT-AATTTAATTAAA
2227 CTTAATTAATTTAATTAAA
1 CTTAATTAATTTAATTAAA
* *
2246 CCTAATTAACTTAA
1 CTTAATTAATTTAA
2260 CCTTAATGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 22 0.76
20 7 0.24
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.43
Consensus pattern (19 bp):
CTTAATTAATTTAATTAAA
Found at i:9785 original size:18 final size:19
Alignment explanation
Indices: 9746--9789 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
9736 AGAAAAGTAA
9746 TAAAATGTGCATAATAAAAT
1 TAAAATGT-CATAATAAAAT
9766 TAAAATGT-ATAA-AAATAT
1 TAAAATGTCATAATAAA-AT
9784 TAAAAT
1 TAAAAT
9790 TAAATTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
20 8 0.35
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (19 bp):
TAAAATGTCATAATAAAAT
Found at i:10586 original size:14 final size:14
Alignment explanation
Indices: 10567--10617 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
10557 CGTTCATCTT
10567 TTTTCTTTTCTTAA
1 TTTTCTTTTCTTAA
*
10581 TTTTCTTTTCGATT-C
1 TTTTCTTTTC--TTAA
10596 TTTT-TTTT-TTAA
1 TTTTCTTTTCTTAA
10608 TTTTCTTTTC
1 TTTTCTTTTC
10618 CATTTGACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
11 2 0.07
12 4 0.13
13 4 0.13
14 14 0.47
15 4 0.13
16 2 0.07
ACGTcount: A:0.10, C:0.14, G:0.02, T:0.75
Consensus pattern (14 bp):
TTTTCTTTTCTTAA
Found at i:12830 original size:16 final size:17
Alignment explanation
Indices: 12806--12855 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
12796 ATTTATAAGT
*
12806 TTATGAAAAT-TAAAAA
1 TTATAAAAATATAAAAA
*
12822 TTATAAAAATATATAAA
1 TTATAAAAATATAAAAA
*
12839 TATATAAATATATAAAA
1 T-TATAAAAATATAAAA
12856 CTAATAAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 9 0.32
17 6 0.21
18 13 0.46
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
TTATAAAAATATAAAAA
Found at i:22363 original size:6 final size:6
Alignment explanation
Indices: 22354--22380 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
22344 GAGAGACAGA
22354 GATAGG GATAGG GATAGG GATAGG GAT
1 GATAGG GATAGG GATAGG GATAGG GAT
22381 CGGTATCGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.48, T:0.19
Consensus pattern (6 bp):
GATAGG
Found at i:23601 original size:26 final size:25
Alignment explanation
Indices: 23548--23602 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
23538 ATAAACATCA
* *
23548 TTTTATCTTTTAATTTAATTTAATT
1 TTTTATCTTTTAAATTAATTTAAGT
* *
23573 TTTTATTTTTTAGAATTAATTTTAGT
1 TTTTATCTTTTA-AATTAATTTAAGT
23599 TTTT
1 TTTT
23603 TTTAAGTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTTATCTTTTAAATTAATTTAAGT
Found at i:23601 original size:27 final size:25
Alignment explanation
Indices: 23548--23603 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
23538 ATAAACATCA
*
23548 TTTTATCTTTTAATTTAATTTAATT
1 TTTTATCTTTTAAATTAATTTAATT
* *
23573 TTTTATTTTTTAGAATTAATTTTAGTT
1 TTTTATCTTTTA-AATTAA-TTTAATT
23600 TTTT
1 TTTT
23604 TTAAGTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 11 0.42
26 5 0.19
27 10 0.38
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (25 bp):
TTTTATCTTTTAAATTAATTTAATT
Found at i:27970 original size:5 final size:6
Alignment explanation
Indices: 27953--27977 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27943 GTATATGGAA
27953 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
27978 GATATAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:29751 original size:20 final size:20
Alignment explanation
Indices: 29713--29751 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
29703 GTGGTTAAGA
29713 TCCTCAAATGCTTTATTTCCC
1 TCCTCAAAT-CTTTATTTCCC
29734 TCCTCAAAT-TTGTATTTC
1 TCCTCAAATCTT-TATTTC
29752 TGAGAAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 6 0.35
21 9 0.53
ACGTcount: A:0.21, C:0.28, G:0.05, T:0.46
Consensus pattern (20 bp):
TCCTCAAATCTTTATTTCCC
Done.