Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007555.1 Kokia drynarioides strain JFW-HI SEQ_122183, 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: 57634
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:14606 original size:15 final size:15
Alignment explanation
Indices: 14583--14617 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
14573 TGAAAATTTG
*
14583 AAAAATATACTTTTT
1 AAAAATATAATTTTT
*
14598 AAAATTATAATTTTT
1 AAAAATATAATTTTT
14613 AAAAA
1 AAAAA
14618 AATATATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAAATATAATTTTT
Found at i:34717 original size:30 final size:30
Alignment explanation
Indices: 34681--34745 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
34671 CAACTTAACA
*
34681 AACAAATGTCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
*
34711 AACAAATGCCTCTAAAATAATAACAATATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
34741 AACAA
1 AACAA
34746 TAAAATAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.57, C:0.15, G:0.03, T:0.25
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:36095 original size:7 final size:7
Alignment explanation
Indices: 36083--36111 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
36073 GAAAGTTAAT
36083 GTGTTTG
1 GTGTTTG
36090 GTGTTTG
1 GTGTTTG
36097 GTGTTTG
1 GTGTTTG
36104 GTGTTTG
1 GTGTTTG
36111 G
1 G
36112 GAGGATGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (7 bp):
GTGTTTG
Found at i:43277 original size:25 final size:25
Alignment explanation
Indices: 43255--43303 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
43245 TTATTAAATA
*
43255 AAAAATAATATAATATTTTTAAAAG
1 AAAAATAAAATAATATTTTTAAAAG
*
43280 TAAAATAAAATAATA-TTTTAAAAG
1 AAAAATAAAATAATATTTTTAAAAG
43304 TAATTGAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
AAAAATAAAATAATATTTTTAAAAG
Found at i:43357 original size:19 final size:19
Alignment explanation
Indices: 43333--43374 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
43323 ACATAATATA
*
43333 TTTAATTA-TTTTTTAAAAT
1 TTTAATTACTCTTTT-AAAT
43352 TTTAATTACTCTTTTAAAT
1 TTTAATTACTCTTTTAAAT
43371 TTTA
1 TTTA
43375 TGTTGATGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTAATTACTCTTTTAAAT
Found at i:44624 original size:27 final size:28
Alignment explanation
Indices: 44594--44646 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
44584 ATATATTATT
* *
44594 TAATTTA-TATCATATAAAAAATAAATA
1 TAATTTATTATAATACAAAAAATAAATA
*
44621 TAATTTATTATAATACAAAAATTAAA
1 TAATTTATTATAATACAAAAAATAAA
44647 AATTAAATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (28 bp):
TAATTTATTATAATACAAAAAATAAATA
Found at i:47270 original size:21 final size:22
Alignment explanation
Indices: 47224--47283 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
47214 CGATCTGAGG
*
47224 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
47245 AAAAATAAAAGAAAATATAATT
1 AAAAATAAAAGAAAATAGAATT
*
47267 AAAAGA-AATAGAAAATA
1 AAAA-ATAAAAGAAAATA
47284 AGAAAGTCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.32
22 22 0.65
23 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:48975 original size:31 final size:32
Alignment explanation
Indices: 48940--49028 Score: 103
Period size: 31 Copynumber: 2.9 Consensus size: 32
48930 GGAATCAAAT
48940 ATTCATATTTGCATTATCATACCTTGTAATC-
1 ATTCATATTTGCATTATCATACCTTGTAATCG
* * * *
48971 ATTCATATTTAC-CTGTCATACCATGTAATCG
1 ATTCATATTTGCATTATCATACCTTGTAATCG
* *
49002 A-TCACATTTGCATTTTCATACCTTGTA
1 ATTCATATTTGCATTATCATACCTTGTA
49029 CATTGTACTA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
30 23 0.49
31 24 0.51
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (32 bp):
ATTCATATTTGCATTATCATACCTTGTAATCG
Found at i:53337 original size:23 final size:23
Alignment explanation
Indices: 53298--53346 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
53288 ATGATAAACC
* *
53298 TTAAAATTAATATAATTCTTTTT
1 TTAAAATTAATATAATTATTTCT
*
53321 TTAAAATTATTGA-AATTATTTCT
1 TTAAAATTAAT-ATAATTATTTCT
53344 TTA
1 TTA
53347 TCTATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (23 bp):
TTAAAATTAATATAATTATTTCT
Found at i:56289 original size:14 final size:15
Alignment explanation
Indices: 56263--56292 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56253 AAGATCTAAT
56263 AAAAGAAACAAACAA
1 AAAAGAAACAAACAA
56278 AAAAGAAA-AAACAA
1 AAAAGAAACAAACAA
56292 A
1 A
56293 GTCTCCCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (15 bp):
AAAAGAAACAAACAA
Done.