Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006583.1 Kokia drynarioides strain JFW-HI SEQ_121171, 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: 63105
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:4585 original size:46 final size:46
Alignment explanation
Indices: 4518--4610 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
4508 GGAACTTAAA
4518 TTACTTGGTACTAGTTTTGGACCAGAATGTTATCGACTTCCATGGT
1 TTACTTGGTACTAGTTTTGGACCAGAATGTTATCGACTTCCATGGT
4564 TTACTTGGTACTAGTTTTGGACCAGAATGTTATCGACTTCCATGGT
1 TTACTTGGTACTAGTTTTGGACCAGAATGTTATCGACTTCCATGGT
4610 T
1 T
4611 ATAATCCTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (46 bp):
TTACTTGGTACTAGTTTTGGACCAGAATGTTATCGACTTCCATGGT
Found at i:10341 original size:3 final size:3
Alignment explanation
Indices: 10333--10360 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
10323 CGCTTGTTTG
10333 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
10361 CATTTGTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:12976 original size:19 final size:19
Alignment explanation
Indices: 12938--12977 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12928 TTTTGAAAAT
*
12938 TATATAAATCATAAAGTTA
1 TATATAAATCAAAAAGTTA
* *
12957 TATATAAATTAAAAATTTA
1 TATATAAATCAAAAAGTTA
12976 TA
1 TA
12978 AAGAGCCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (19 bp):
TATATAAATCAAAAAGTTA
Found at i:13268 original size:3 final size:3
Alignment explanation
Indices: 13260--13287 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
13250 ATGTATTTTT
13260 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
13288 CCTGATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:29785 original size:25 final size:25
Alignment explanation
Indices: 29749--29799 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
29739 TATAATTCAA
29749 AGAACAAGAATAAAGTGAAAGAATG
1 AGAACAAGAATAAAGTGAAAGAATG
* *
29774 AGAACAATAATAAATTGAAAGAATG
1 AGAACAAGAATAAAGTGAAAGAATG
29799 A
1 A
29800 AAAATGACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.61, C:0.04, G:0.20, T:0.16
Consensus pattern (25 bp):
AGAACAAGAATAAAGTGAAAGAATG
Found at i:37672 original size:25 final size:27
Alignment explanation
Indices: 37635--37689 Score: 87
Period size: 25 Copynumber: 2.1 Consensus size: 27
37625 TGAACAATGG
37635 TTTAATGTGCAATTGTATACATG-AAT
1 TTTAATGTGCAATTGTATACATGAAAT
*
37661 TTTAAT-TGCAATTTTATACATGAAAT
1 TTTAATGTGCAATTGTATACATGAAAT
37687 TTT
1 TTT
37690 GTTTGATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.47
Consensus pattern (27 bp):
TTTAATGTGCAATTGTATACATGAAAT
Found at i:38088 original size:17 final size:18
Alignment explanation
Indices: 38058--38091 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38048 TAGAAACCTG
38058 TTTTAAATTGTTATTAAC
1 TTTTAAATTGTTATTAAC
*
38076 TTTT-AATTTTTATTAA
1 TTTTAAATTGTTATTAA
38092 TCTATCTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTAAATTGTTATTAAC
Found at i:41625 original size:23 final size:24
Alignment explanation
Indices: 41585--41635 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
41575 GAAAAATAGT
*
41585 TTTTGGGGTTTAGAGGAA-AAAAA
1 TTTTGGAGTTTAGAGGAAGAAAAA
*
41608 TTTTGGAGTTTA-AGGGAAGCAAAA
1 TTTTGGAGTTTAGA-GGAAGAAAAA
41632 TTTT
1 TTTT
41636 TTAGAGGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.04
23 15 0.62
24 8 0.33
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.35
Consensus pattern (24 bp):
TTTTGGAGTTTAGAGGAAGAAAAA
Found at i:42007 original size:19 final size:18
Alignment explanation
Indices: 41969--42007 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
41959 TATAGTAAGG
*
41969 TATTAAAAAAAACATAAA
1 TATTAAAAAAAACACAAA
41987 TATTAAAAAAAACACATAA
1 TATTAAAAAAAACACA-AA
42006 TA
1 TA
42008 ATTTTTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (18 bp):
TATTAAAAAAAACACAAA
Found at i:43537 original size:19 final size:19
Alignment explanation
Indices: 43513--43549 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
43503 TATTATTATT
*
43513 ATATTTATAATTGAAATAA
1 ATATTTATAATTAAAATAA
*
43532 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
43550 TTAATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:43570 original size:15 final size:14
Alignment explanation
Indices: 43529--43570 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
43519 ATAATTGAAA
*
43529 TAAATATTTATTAT
1 TAAATATTTAATAT
43543 TAAA-ATATTAATAT
1 TAAATAT-TTAATAT
43557 TAAATATTTCAATA
1 TAAATATTT-AATA
43571 ATATTTGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 2 0.08
14 16 0.67
15 6 0.25
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAATATTTAATAT
Found at i:44017 original size:20 final size:20
Alignment explanation
Indices: 43989--44084 Score: 71
Period size: 20 Copynumber: 4.9 Consensus size: 20
43979 TCACGTCAGC
*
43989 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
* *
44009 AAATTATTTTTAAAA-AAATA
1 AAATTA-TTTTAAAATTATTA
44029 AAATTA--TTAAAATTATTTTTTA
1 AAATTATTTTAAAATTA----TTA
44051 AAA-TA---TAAAATTATTA
1 AAATTATTTTAAAATTATTA
44067 AAATTATTTTAAAATTAT
1 AAATTATTTTAAAATTAT
44085 AATCATCATC
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
16 6 0.10
17 8 0.13
18 1 0.02
20 31 0.51
21 10 0.16
22 5 0.08
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:44030 original size:29 final size:29
Alignment explanation
Indices: 43998--44080 Score: 141
Period size: 29 Copynumber: 2.9 Consensus size: 29
43988 CAAATGATTT
43998 TAAAATTATTAAAATTATTTTTAAAAAAA
1 TAAAATTATTAAAATTATTTTTAAAAAAA
* *
44027 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTAAAAAAA
44056 TAAAATTATTAAAATTA-TTTTAAAA
1 TAAAATTATTAAAATTATTTTTAAAA
44081 TTATAATCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 7 0.14
29 44 0.86
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTAAAAAAA
Found at i:44927 original size:18 final size:19
Alignment explanation
Indices: 44896--44932 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
44886 TATTATTTCA
*
44896 AAAAAATAATTTTATAATT
1 AAAAAATAATTTTAAAATT
44915 AAAAAATAA-TTTAAAATT
1 AAAAAATAATTTTAAAATT
44933 TTTATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAAATAATTTTAAAATT
Found at i:56593 original size:2 final size:2
Alignment explanation
Indices: 56582--56618 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
56572 TGGTGCCACA
*
56582 AT AT -T AT AT AT AT AT AT AT AT AT AT AT GT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56619 AAACTGGGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:57350 original size:19 final size:18
Alignment explanation
Indices: 57299--57350 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
57289 AAAATTATTA
*
57299 TTTTAAAAATTTTGAATT
1 TTTTAAAATTTTTGAATT
*
57317 TTTGAAAATTATTTGAATT
1 TTTTAAAATT-TTTGAATT
57336 TTTTAATAATTTTTG
1 TTTTAA-AATTTTTG
57351 TTGAGATAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 8 0.28
19 17 0.59
20 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (18 bp):
TTTTAAAATTTTTGAATT
Found at i:58348 original size:3 final size:3
Alignment explanation
Indices: 58329--58366 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
58319 CCAAAACCAT
*
58329 TCC TCC TTC T-C TCCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC T-CC TCC TCC TCC TCC TCC TCC TCC TC
58367 TATATCCGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.88
4 2 0.06
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (3 bp):
TCC
Found at i:62163 original size:5 final size:5
Alignment explanation
Indices: 62153--62177 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
62143 TTATCATCAC
62153 CTCCA CTCCA CTCCA CTCCA CTCCA
1 CTCCA CTCCA CTCCA CTCCA CTCCA
62178 GACACGTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.00, T:0.20
Consensus pattern (5 bp):
CTCCA
Done.