Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007583.1 Kokia drynarioides strain JFW-HI SEQ_122213, 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: 17883
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:991 original size:18 final size:20
Alignment explanation
Indices: 970--1008 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
960 TGAGTTTGAA
970 TTTTTAAT-AAATAT-TAAT
1 TTTTTAATCAAATATATAAT
*
988 TTTTTATTCAAATATATAAT
1 TTTTTAATCAAATATATAAT
1008 T
1 T
1009 ATAGGTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 6 0.33
20 5 0.28
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTTAATCAAATATATAAT
Found at i:1243 original size:16 final size:18
Alignment explanation
Indices: 1222--1262 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
1212 AAATAGTTTT
*
1222 TTAATTATAAA-TTTAA-
1 TTAATTAAAAATTTTAAG
1238 TTAATTAAAAATTTTAAG
1 TTAATTAAAAATTTTAAG
1256 TTAATTA
1 TTAATTA
1263 CACCTTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.45
17 5 0.23
18 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TTAATTAAAAATTTTAAG
Found at i:1483 original size:15 final size:15
Alignment explanation
Indices: 1463--1513 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
1453 ACAAAATAAT
1463 AATATAACTGATTAA
1 AATATAACTGATTAA
*
1478 AATATAAC--ATTTCA
1 AATATAACTGA-TTAA
*
1492 AATATAAGTGATTAA
1 AATATAACTGATTAA
1507 AATATAA
1 AATATAA
1514 TCTAAAGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.03
14 10 0.33
15 18 0.60
16 1 0.03
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (15 bp):
AATATAACTGATTAA
Found at i:1486 original size:31 final size:29
Alignment explanation
Indices: 1451--1513 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
1441 AACTATTTCG
1451 TAACAAAATAATAATATAACTGATTAAAATA
1 TAAC-AAATAA-AATATAACTGATTAAAATA
** * *
1482 TAACATTTCAAATATAAGTGATTAAAATA
1 TAACAAATAAAATATAACTGATTAAAATA
1511 TAA
1 TAA
1514 TCTAAAGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 21 0.75
30 3 0.11
31 4 0.14
ACGTcount: A:0.57, C:0.06, G:0.05, T:0.32
Consensus pattern (29 bp):
TAACAAATAAAATATAACTGATTAAAATA
Found at i:4369 original size:19 final size:19
Alignment explanation
Indices: 4342--4382 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
4332 GTTGAATTGA
*
4342 TTAAATTTAATTAATTTAT
1 TTAAATTTAATTAATTAAT
* *
4361 TTAATTTTAATTTATTAAT
1 TTAAATTTAATTAATTAAT
4380 TTA
1 TTA
4383 TTAAAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAAATTTAATTAATTAAT
Found at i:4372 original size:15 final size:14
Alignment explanation
Indices: 4352--4381 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
4342 TTAAATTTAA
4352 TTAATTTATTTAATT
1 TTAATTTA-TTAATT
4367 TTAATTTATTAATT
1 TTAATTTATTAATT
4381 T
1 T
4382 ATTAAAATTT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTAATTTATTAATT
Found at i:4392 original size:23 final size:24
Alignment explanation
Indices: 4345--4392 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
4335 GAATTGATTA
* *
4345 AATTTAATTAATTTATTTAATTTT
1 AATTTAATTAATTTATTAAAATTT
4369 AATTT-ATTAATTTATTAAAATTT
1 AATTTAATTAATTTATTAAAATTT
4392 A
1 A
4393 TAGATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
AATTTAATTAATTTATTAAAATTT
Found at i:4393 original size:10 final size:8
Alignment explanation
Indices: 4345--4386 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
4335 GAATTGATTA
4345 AATTTAATT
1 AATTT-ATT
4354 AATTTATTT
1 AATTTA-TT
4363 AA-TT-TT
1 AATTTATT
4369 AATTTATT
1 AATTTATT
4377 AATTTATT
1 AATTTATT
4385 AA
1 AA
4387 AATTTATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
6 4 0.13
7 2 0.07
8 15 0.50
9 9 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
AATTTATT
Found at i:4732 original size:25 final size:27
Alignment explanation
Indices: 4693--4746 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
4683 TAACAAAGTG
*
4693 AAATAAATTTTAAAAAATATAT-ACTT
1 AAATAAATATTAAAAAATATATAACTT
*
4719 AAAT-AATATTAAAATATATATAACTT
1 AAATAAATATTAAAAAATATATAACTT
4745 AA
1 AA
4747 CAAATAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (27 bp):
AAATAAATATTAAAAAATATATAACTT
Found at i:4752 original size:26 final size:24
Alignment explanation
Indices: 4697--4752 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
4687 AAAGTGAAAT
*
4697 AAATTTTAAAAAATATATACTTAA
1 AAATATTAAAAAATATATACTTAA
*
4721 ATAATATTAAAATATATATAACTTAA
1 A-AATATTAAAAAATATAT-ACTTAA
4747 CAAATA
1 -AAATA
4753 AATGTCTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 1 0.04
25 15 0.56
26 10 0.37
27 1 0.04
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATATTAAAAAATATATACTTAA
Found at i:4841 original size:22 final size:22
Alignment explanation
Indices: 4793--4864 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
4783 TAAAATAAGT
4793 AATAACAACAAAATAGTAATAA
1 AATAACAACAAAATAGTAATAA
* * * * *
4815 CATAATAATAAAATTGTAGTAA
1 AATAACAACAAAATAGTAATAA
* * * *
4837 AATAAGAA-AAAACAATAAGAA
1 AATAACAACAAAATAGTAATAA
4858 AATAACA
1 AATAACA
4865 GATTTTTTTT
Statistics
Matches: 37, Mismatches: 13, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
21 14 0.38
22 23 0.62
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.19
Consensus pattern (22 bp):
AATAACAACAAAATAGTAATAA
Found at i:4972 original size:17 final size:18
Alignment explanation
Indices: 4938--4982 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
4928 ATTTGACTTT
*
4938 TTTTTTAAATAGATTTAA
1 TTTTTTAAATAGAATTAA
*
4956 TTTTTTACATA-AATTAA
1 TTTTTTAAATAGAATTAA
*
4973 TTTTTCAAAT
1 TTTTTTAAAT
4983 TTATATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTTTTAAATAGAATTAA
Found at i:8415 original size:12 final size:13
Alignment explanation
Indices: 8398--8430 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
8388 CAATTATTGT
8398 AAATTATTA-ATA
1 AAATTATTATATA
8410 AAATTATTATATA
1 AAATTATTATATA
*
8423 ATATTATT
1 AAATTATT
8431 TTATGTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATTATTATATA
Found at i:8738 original size:18 final size:19
Alignment explanation
Indices: 8703--8740 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
8693 TTTGTCCCCA
*
8703 TTTTCAAAAGTTGTAATTT
1 TTTTCAAAAGTTGAAATTT
*
8722 TTTTCAATA-TTGAAATTT
1 TTTTCAAAAGTTGAAATTT
8740 T
1 T
8741 AAAATTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (19 bp):
TTTTCAAAAGTTGAAATTT
Found at i:11661 original size:29 final size:30
Alignment explanation
Indices: 11607--11676 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
11597 ATCCCAAAAC
*
11607 TATATATGAACTATAATTTAATGTGCAATTG
1 TATACATGAACTATAATTT-ATGTGCAATTG
* * *
11638 TATACGTGAACTTTAATTT-TGTGCAATTT
1 TATACATGAACTATAATTTATGTGCAATTG
11667 TATACATGAA
1 TATACATGAA
11677 TTTTTTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (30 bp):
TATACATGAACTATAATTTATGTGCAATTG
Found at i:11865 original size:31 final size:30
Alignment explanation
Indices: 11829--11897 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
11819 AATTAAATTA
11829 AAATTAAAGTTTCA-A-GTATACATTTGAACC
1 AAATTAAAGTTTCACATGTATA-A-TTGAACC
* *
11859 ACAATTAGAGTTTCACATGTATAATTGCACC
1 A-AATTAAAGTTTCACATGTATAATTGAACC
11890 AAATTAAA
1 AAATTAAA
11898 ATTCATGTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
30 7 0.21
31 19 0.58
32 2 0.06
33 5 0.15
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.32
Consensus pattern (30 bp):
AAATTAAAGTTTCACATGTATAATTGAACC
Found at i:13230 original size:2 final size:2
Alignment explanation
Indices: 13223--13257 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
13213 TGTGGGTGGG
13223 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
13258 TTTACCATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:14090 original size:42 final size:42
Alignment explanation
Indices: 14010--14091 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
14000 ATAAGTGTAT
* *
14010 TTTTGTTATTATCCAATTGAGTTGATATTTAGACTTGTGATA
1 TTTTGTTATTATCCAATTGAGTTGATACTTAAACTTGTGATA
** * *
14052 TTTTGTTATTATTTAATTGATTTGATACTTAAATTTGTGA
1 TTTTGTTATTATCCAATTGAGTTGATACTTAAACTTGTGA
14092 CATCATCTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.54
Consensus pattern (42 bp):
TTTTGTTATTATCCAATTGAGTTGATACTTAAACTTGTGATA
Done.