Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011118.1 Kokia drynarioides strain JFW-HI SEQ_126091, 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: 21904
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Warning! 46 characters in sequence are not A, C, G, or T
Found at i:2047 original size:20 final size:21
Alignment explanation
Indices: 2008--2047 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1998 ATTAAAAATA
*
2008 TTAAAATCATTATTAAATTAT
1 TTAAAATAATTATTAAATTAT
*
2029 TTAAAATAATT-TTATATTA
1 TTAAAATAATTATTAAATTA
2048 AATAATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAAATAATTATTAAATTAT
Found at i:4727 original size:22 final size:20
Alignment explanation
Indices: 4697--4737 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
4687 TTAAATAATT
*
4697 TTTATTTTTAAAGTTTCTTAAA
1 TTTAATTTTAAA-TTT-TTAAA
4719 TTTAATTTTAAATTTTTAA
1 TTTAATTTTAAATTTTTAA
4738 GAATCAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 3 0.17
22 11 0.61
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTAATTTTAAATTTTTAAA
Found at i:6091 original size:29 final size:29
Alignment explanation
Indices: 6049--6107 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
6039 GGAAGGGGCC
*
6049 ATGTGTTTTATCCGTATATTGTATTCCTT
1 ATGTGTTTTATCCGTATATTGTACTCCTT
6078 ATGTGTTTTATCCGTATATTGTACTCCTT
1 ATGTGTTTTATCCGTATATTGTACTCCTT
6107 A
1 A
6108 ATATTTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.19, C:0.15, G:0.14, T:0.53
Consensus pattern (29 bp):
ATGTGTTTTATCCGTATATTGTACTCCTT
Found at i:8706 original size:24 final size:24
Alignment explanation
Indices: 8690--8757 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
8680 TAACTAAAAT
8690 AAATAAACAGAATTTAATTGAAAC
1 AAATAAACAGAATTTAATTGAAAC
*
8714 AAATAAACATAATTTAATTGAAAC
1 AAATAAACAGAATTTAATTGAAAC
* *
8738 AAATAAATAGAGTTTAATTG
1 AAATAAACAGAATTTAATTG
8758 GAAGATTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (24 bp):
AAATAAACAGAATTTAATTGAAAC
Found at i:9474 original size:14 final size:14
Alignment explanation
Indices: 9455--9503 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
9445 GTTCATCTCC
9455 TCTCTTTTCTTAGT
1 TCTCTTTTCTTAGT
9469 TCTCTTTTCATCTA-T
1 TCTCTTTTC-T-TAGT
9484 TCT-TTTT-TTAGT
1 TCTCTTTTCTTAGT
*
9496 TTTCTTTT
1 TCTCTTTT
9504 TCATTTGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
11 2 0.07
12 4 0.13
13 4 0.13
14 13 0.43
15 5 0.17
16 2 0.07
ACGTcount: A:0.08, C:0.18, G:0.04, T:0.69
Consensus pattern (14 bp):
TCTCTTTTCTTAGT
Found at i:10130 original size:26 final size:26
Alignment explanation
Indices: 10083--10132 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
10073 CAGTCAAATG
10083 AAAAAAAACTAAAAAAAGAAGAGACA
1 AAAAAAAACTAAAAAAAGAAGAGACA
*
10109 AAAAGAAAACTAAGAAAA-AAGAGA
1 AAAA-AAAACTAAAAAAAGAAGAGA
10133 GGAGATGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (26 bp):
AAAAAAAACTAAAAAAAGAAGAGACA
Found at i:15453 original size:18 final size:19
Alignment explanation
Indices: 15432--15470 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
15422 CTAAAAATAG
15432 TTTTTGAAAAATAAAT-TT
1 TTTTTGAAAAATAAATATT
* *
15450 TTTTTTAAAAGTAAATATT
1 TTTTTGAAAAATAAATATT
15469 TT
1 TT
15471 ATGGTATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTTTGAAAAATAAATATT
Found at i:15932 original size:15 final size:16
Alignment explanation
Indices: 15911--15959 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 16
15901 TATACTACAA
15911 AATATTTATTATTAAT
1 AATATTTATTATTAAT
*
15927 -ATATTTATAATTGTAAT
1 AATATTTATTA-T-TAAT
15944 AAATATTTATTATTAA
1 -AATATTTATTATTAA
15960 ATTATTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 9 0.33
16 1 0.04
17 7 0.26
18 1 0.04
19 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
AATATTTATTATTAAT
Found at i:16024 original size:16 final size:16
Alignment explanation
Indices: 15993--16029 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
15983 AAGTGAATAA
15993 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
16009 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
16025 TATTA
1 TATTA
16030 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:16051 original size:18 final size:18
Alignment explanation
Indices: 16015--16050 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
16005 TTATTATTTT
*
16015 TAAAATTTATTATTAAAA
1 TAAAATTTAATATTAAAA
16033 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
16051 TGATTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:16847 original size:17 final size:17
Alignment explanation
Indices: 16812--16853 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
16802 GGAAAAAGTA
*
16812 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
16830 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
16847 GTTAAAG
1 GTTAAAG
16854 GAAGGGAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:20568 original size:6 final size:6
Alignment explanation
Indices: 20559--20623 Score: 64
Period size: 6 Copynumber: 11.3 Consensus size: 6
20549 CAAATTTATT
* * **
20559 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
20605 TTT-AA TTAAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
20624 GATTTAAAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
5 10 0.22
6 36 0.78
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:20580 original size:17 final size:17
Alignment explanation
Indices: 20550--20640 Score: 101
Period size: 17 Copynumber: 5.3 Consensus size: 17
20540 AAATTGATTC
20550 AAATTTATTTTTAAATTT
1 AAATTTA-TTTTAAATTT
*
20568 AGATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
**
20585 AAATTTGCTTTAAATTT
1 AAATTTATTTTAAATTT
* *
20602 AAATTTAATTAAAATTT
1 AAATTTATTTTAAATTT
* * *
20619 AAATTGATTTAAAACTT
1 AAATTTATTTTAAATTT
20636 AAATT
1 AAATT
20641 AAAAGTCCAA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
17 57 0.90
18 6 0.10
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:20585 original size:23 final size:23
Alignment explanation
Indices: 20536--20609 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
20526 CTTTTATTGG
* *
20536 ATTTAAA-TTGATTCAAATTTAT
1 ATTTAAATTTGATTTAAATTTAA
* *
20558 TTTTAAATTTAGATTT-ATTTTAA
1 ATTTAAATTT-GATTTAAATTTAA
*
20581 ATTTAAATTTGCTTTAAATTTAA
1 ATTTAAATTTGATTTAAATTTAA
20604 ATTTAA
1 ATTTAA
20610 TTAAAATTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
22 10 0.24
23 28 0.67
24 4 0.10
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (23 bp):
ATTTAAATTTGATTTAAATTTAA
Found at i:21296 original size:3 final size:3
Alignment explanation
Indices: 21283--21367 Score: 134
Period size: 3 Copynumber: 28.0 Consensus size: 3
21273 AATTTATTAT
21283 TAA TAA GTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
21329 TAA TAA TAA TAA TAA TAA TAA TAA CAA CAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21368 ACGGTGGTAA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
3 74 0.96
4 3 0.04
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Done.