Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000100.1 Kokia drynarioides strain JFW-HI SEQ_110734, 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: 36777
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:114 original size:17 final size:18
Alignment explanation
Indices: 92--127 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
82 TAAATGAGTT
92 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
109 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
127 A
1 A
128 TAAAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:2014 original size:26 final size:26
Alignment explanation
Indices: 1985--2042 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
1975 TGTCATTTGC
*
1985 TAAACCTCATTAAATAAATTCAAATA
1 TAAACATCATTAAATAAATTCAAATA
* * *
2011 TAAAAATTATTAAATAAATTCAAATT
1 TAAACATCATTAAATAAATTCAAATA
2037 TAAACA
1 TAAACA
2043 AAATTAATTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (26 bp):
TAAACATCATTAAATAAATTCAAATA
Found at i:2048 original size:26 final size:26
Alignment explanation
Indices: 1993--2049 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
1983 GCTAAACCTC
*
1993 ATTAAATAAATTCAAATATAAAAATT
1 ATTAAATAAATTCAAATATAAAAATA
*
2019 ATTAAATAAATTCAAATTTAAACAA-A
1 ATTAAATAAATTCAAATATAAA-AATA
2045 ATTAA
1 ATTAA
2050 TTCCAAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.33
Consensus pattern (26 bp):
ATTAAATAAATTCAAATATAAAAATA
Found at i:4863 original size:26 final size:26
Alignment explanation
Indices: 4834--4888 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
4824 TCTGCTAACC
*
4834 TTTTGTTTCCTTTCCTTCTTCAAAAA
1 TTTTGTTTCCTTTCCTTCTTAAAAAA
*
4860 TTTTGTTTCCTTTTCTTCTTAAAAAA
1 TTTTGTTTCCTTTCCTTCTTAAAAAA
4886 TTT
1 TTT
4889 GCTGTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.20, C:0.18, G:0.04, T:0.58
Consensus pattern (26 bp):
TTTTGTTTCCTTTCCTTCTTAAAAAA
Found at i:5330 original size:2 final size:2
Alignment explanation
Indices: 5323--5358 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5313 ATGGATTAAA
*
5323 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5359 TATTTAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:6568 original size:20 final size:20
Alignment explanation
Indices: 6510--6568 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
6500 AAAAAAAAAA
6510 TATTTAGAAAAT-TTAAAATT
1 TATTTA-AAAATATTAAAATT
* *
6530 TATTT-AAAATAGATAAAAAT
1 TATTTAAAAATA-TTAAAATT
6550 TATTTTAAAAATATTAAAA
1 TA-TTTAAAAATATTAAAA
6569 GTTGTAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 5 0.16
20 13 0.41
21 8 0.25
22 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
TATTTAAAAATATTAAAATT
Found at i:12798 original size:3 final size:3
Alignment explanation
Indices: 12784--12845 Score: 70
Period size: 3 Copynumber: 19.7 Consensus size: 3
12774 TTGGGTAACT
* *
12784 ATG ATG AAG ATG ATG ATG ATG ATG ATG ATG ACTTG CTTG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A--TG -ATG ATG ATG ATG
*
12832 ATG ATG AGG ATG AT
1 ATG ATG ATG ATG AT
12846 TATAATGAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
3 46 0.92
4 2 0.04
5 2 0.04
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:16055 original size:17 final size:17
Alignment explanation
Indices: 16023--16056 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16013 CACATCTCAG
*
16023 CACCTAATATAGATATT
1 CACCTAATACAGATATT
*
16040 CACCTAATACATATATT
1 CACCTAATACAGATATT
16057 AACAGATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.35
Consensus pattern (17 bp):
CACCTAATACAGATATT
Found at i:21497 original size:15 final size:15
Alignment explanation
Indices: 21479--21530 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
21469 ACTACAAAAC
21479 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
21494 ATTTATAACTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
21513 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
21528 ATT
1 ATT
21531 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:21560 original size:28 final size:26
Alignment explanation
Indices: 21529--21583 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
21519 TATTAAAATA
*
21529 TTAATATTGAATATTTTCAAAATATTAT
1 TTAAAATT-AATATTTTCAAAAT-TTAT
* *
21557 TTAAAATTATTATTTTTAAAATTTAT
1 TTAAAATTAATATTTTCAAAATTTAT
21583 T
1 T
21584 ATTAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.21
27 12 0.50
28 7 0.29
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (26 bp):
TTAAAATTAATATTTTCAAAATTTAT
Found at i:21582 original size:16 final size:16
Alignment explanation
Indices: 21551--21587 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
21541 ATTTTCAAAA
21551 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
21567 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
21583 TATTA
1 TATTA
21588 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:23714 original size:54 final size:55
Alignment explanation
Indices: 23632--23741 Score: 186
Period size: 54 Copynumber: 2.0 Consensus size: 55
23622 TGGATTTATA
* *
23632 CACTTAATAATCTTAAATCGAATTTGATTTAAAAAAAA-TATTTCTATCTTAAAT
1 CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAAAGTATTTCAATCTTAAAT
23686 CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAAATGTATTTCAATCTTAAAT
1 CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAAA-GTATTTCAATCTTAAAT
23742 TAGTTGACAA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
54 37 0.71
56 15 0.29
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (55 bp):
CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAAAGTATTTCAATCTTAAAT
Found at i:26103 original size:19 final size:21
Alignment explanation
Indices: 26068--26106 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
26058 ACACATCATT
26068 ATAAAATTAAGAATAATATTG
1 ATAAAATTAAGAATAATATTG
26089 ATAAAA-TAA-AATAATATT
1 ATAAAATTAAGAATAATATT
26107 ATTATTGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
ATAAAATTAAGAATAATATTG
Found at i:31465 original size:53 final size:54
Alignment explanation
Indices: 31380--31484 Score: 167
Period size: 53 Copynumber: 1.9 Consensus size: 54
31370 ATTTATACAT
*
31380 TTAATAATCTTAAATCGAATTTGATT-AAAAAAAGCATTTCAATCTTAAATCAC
1 TTAATAATCTTAAATCAAATTTGATTAAAAAAAAGCATTTCAATCTTAAATCAC
* *
31433 TTAATAATCTTAAATCAAATTTGATTTTAAAAAAAGTATTTCAATCTTAAAT
1 TTAATAATCTTAAATCAAATTTGA-TTAAAAAAAAGCATTTCAATCTTAAAT
31485 TAGTGACAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
53 23 0.48
54 2 0.04
55 23 0.48
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (54 bp):
TTAATAATCTTAAATCAAATTTGATTAAAAAAAAGCATTTCAATCTTAAATCAC
Found at i:32349 original size:18 final size:18
Alignment explanation
Indices: 32322--32359 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
32312 TGAATTTTCG
32322 AATTCAAAT-AACTCGAAT
1 AATTCAAATAAAC-CGAAT
*
32340 AATTCGAATAAACCGAAT
1 AATTCAAATAAACCGAAT
32358 AA
1 AA
32360 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.53, C:0.16, G:0.08, T:0.24
Consensus pattern (18 bp):
AATTCAAATAAACCGAAT
Found at i:34293 original size:33 final size:33
Alignment explanation
Indices: 34251--34316 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
34241 ATAAGCAATA
34251 AGCATTAGAAAATAAAGTCTAGCTCACCATGTT
1 AGCATTAGAAAATAAAGTCTAGCTCACCATGTT
*
34284 AGCATTAGAAAATAAAGTCTAGCTTACCATGTT
1 AGCATTAGAAAATAAAGTCTAGCTCACCATGTT
34317 GTAATCATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (33 bp):
AGCATTAGAAAATAAAGTCTAGCTCACCATGTT
Done.