Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010980.1 Kokia drynarioides strain JFW-HI SEQ_125950, 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: 49487
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:2238 original size:3 final size:3
Alignment explanation
Indices: 2230--2261 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2220 TTTCCTAAAA
2230 TCT TCT TCT TCT TCT TCT TCT TCT TCT T-T TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2262 CATCCTAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:8340 original size:12 final size:12
Alignment explanation
Indices: 8311--8343 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
8301 CTTAATGGAG
*
8311 ATAATGACAAAA
1 ATAATCACAAAA
8323 AT-ATCACAAAA
1 ATAATCACAAAA
8334 ATAATCACAA
1 ATAATCACAA
8344 CCAATTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.64, C:0.15, G:0.03, T:0.18
Consensus pattern (12 bp):
ATAATCACAAAA
Found at i:11736 original size:22 final size:22
Alignment explanation
Indices: 11694--11744 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
11684 TTATAAAATG
*
11694 TTATAATAATTTTCAAGTTTTTA
1 TTAT-ATAATTTTCAAATTTTTA
11717 TTATATAATTTT-AATATTTTTA
1 TTATATAATTTTCAA-ATTTTTA
*
11739 TAATAT
1 TTATAT
11745 GTTTATGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 19 0.76
23 4 0.16
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
TTATATAATTTTCAAATTTTTA
Found at i:11903 original size:17 final size:17
Alignment explanation
Indices: 11873--11919 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
11863 TTTTTTATAA
11873 ATTTATTAAAATTTTAAT-
1 ATTT-TTAAAA-TTTAATC
*
11891 ATTTTTAATATTTAATC
1 ATTTTTAAAATTTAATC
11908 ATTTTTTAAAAT
1 A-TTTTTAAAAT
11920 ATTTCTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 6 0.24
17 6 0.24
18 13 0.52
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTTAAAATTTAATC
Found at i:16679 original size:29 final size:29
Alignment explanation
Indices: 16613--16679 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
16603 TTATGTTAAT
16613 AAATAATT-TCAAAAAATATATAAAAATCA
1 AAATAATTAT-AAAAAATATATAAAAATCA
* * *
16642 AAATGATTATAAAAAATTTATTAAAATTCA
1 AAATAATTATAAAAAATATA-TAAAAATCA
16672 AAA-AATTA
1 AAATAATTA
16680 ACGTCAAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (29 bp):
AAATAATTATAAAAAATATATAAAAATCA
Found at i:17599 original size:2 final size:2
Alignment explanation
Indices: 17592--17621 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17582 AATGATACAC
17592 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17622 GGATTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21606 original size:22 final size:23
Alignment explanation
Indices: 21556--21601 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
21546 ATTATAAAAG
21556 ACTTAAATTAAAAAAATTATCAT
1 ACTTAAATTAAAAAAATTATCAT
*
21579 ACTTAAATTAAAAAATTTATCAT
1 ACTTAAATTAAAAAAATTATCAT
21602 TTTAAGGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (23 bp):
ACTTAAATTAAAAAAATTATCAT
Found at i:22121 original size:20 final size:21
Alignment explanation
Indices: 22083--22121 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22073 AAATTAGAGT
*
22083 GAAATTGTTTGAGTTTTGATA
1 GAAATTGTTAGAGTTTTGATA
22104 GAAATTGTTAGA-TTTTGA
1 GAAATTGTTAGAGTTTTGA
22122 AGCTATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (21 bp):
GAAATTGTTAGAGTTTTGATA
Found at i:22270 original size:21 final size:20
Alignment explanation
Indices: 22236--22275 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
22226 AGCTATTTGA
22236 ATTATTTAATTGAATGAAATT
1 ATTATTTAATTGAA-GAAATT
22257 ATTATTTAGA-TGAAGAAAT
1 ATTATTTA-ATTGAAGAAAT
22276 GAGACAAGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 12 0.67
22 1 0.06
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (20 bp):
ATTATTTAATTGAAGAAATT
Found at i:25352 original size:11 final size:12
Alignment explanation
Indices: 25331--25355 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25321 TTAAATATAT
25331 AAAATTAAAAAA
1 AAAATTAAAAAA
25343 AAAATTAAAAAA
1 AAAATTAAAAAA
25355 A
1 A
25356 CACGTGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATTAAAAAA
Found at i:30610 original size:30 final size:31
Alignment explanation
Indices: 30575--30633 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
30565 TTAATAGTTT
*
30575 ATATTTTTATAATTTTTAA-AAGATTAAATC
1 ATATTTTTATAATTTTTAATAAAATTAAATC
*
30605 ATATTTTTATCATTTTTAATAAAATTAAA
1 ATATTTTTATAATTTTTAATAAAATTAAA
30634 ATATAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (31 bp):
ATATTTTTATAATTTTTAATAAAATTAAATC
Found at i:30644 original size:31 final size:29
Alignment explanation
Indices: 30574--30644 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 29
30564 TTTAATAGTT
*
30574 TATATTTTTATAATTTTTAAAAGATTAAA
1 TATATTTTTATAATTTTTAAAAAATTAAA
*
30603 TCATATTTTTATCATTTTTAATAAAATTAAAA
1 T-ATATTTTTATAATTTTTAA-AAAATT-AAA
*
30635 TATAATTTTA
1 TATATTTTTA
30645 CTTTTACTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 1 0.03
30 18 0.50
31 13 0.36
32 4 0.11
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (29 bp):
TATATTTTTATAATTTTTAAAAAATTAAA
Found at i:33358 original size:23 final size:23
Alignment explanation
Indices: 33313--33359 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
33303 TACATTGTTC
* *
33313 ATGAACATGTTCGATTAAGTTAA
1 ATGAACATGTTCGATGAAATTAA
33336 ATGAACATGTTCG-TGAACATTAA
1 ATGAACATGTTCGATGAA-ATTAA
33359 A
1 A
33360 CAAACAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (23 bp):
ATGAACATGTTCGATGAAATTAA
Found at i:38346 original size:2 final size:2
Alignment explanation
Indices: 38339--38369 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38329 ATAGAACAGA
38339 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
38370 AGAATAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:45280 original size:15 final size:15
Alignment explanation
Indices: 45260--45289 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45250 ATAGTTTAAT
*
45260 AAATTAATTCAAACA
1 AAATTAAGTCAAACA
45275 AAATTAAGTCAAACA
1 AAATTAAGTCAAACA
45290 TTTGCTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.13, G:0.03, T:0.23
Consensus pattern (15 bp):
AAATTAAGTCAAACA
Done.