Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007705.1 Kokia drynarioides strain JFW-HI SEQ_122336, 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: 29536
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Found at i:4145 original size:3 final size:3
Alignment explanation
Indices: 4095--4131 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
4085 TTTAAGGAAG
4095 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
4132 AATAATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:4819 original size:19 final size:18
Alignment explanation
Indices: 4770--4822 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
4760 TAAAAATAAT
*
4770 TATTTAAATTTCAAAA-A
1 TATTTAAATTTTAAAATA
**
4787 TATTTAAAAATTAAAATA
1 TATTTAAATTTTAAAATA
4805 TCATTTAAATTTTAAAAT
1 T-ATTTAAATTTTAAAAT
4823 TATAAAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 13 0.45
18 2 0.07
19 14 0.48
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
TATTTAAATTTTAAAATA
Found at i:6926 original size:23 final size:23
Alignment explanation
Indices: 6896--6940 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
6886 GGTAAATAGT
6896 TATCTATCTTGGTCCATCTGTGC
1 TATCTATCTTGGTCCATCTGTGC
6919 TATCTATCTTGGTCCATCTGTG
1 TATCTATCTTGGTCCATCTGTG
6941 GAGATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.44
Consensus pattern (23 bp):
TATCTATCTTGGTCCATCTGTGC
Found at i:13418 original size:30 final size:31
Alignment explanation
Indices: 13343--13418 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
13333 TTGATCTAAT
* *
13343 TTGGTACTCAAACTTAACACTTTTTCTTAAT
1 TTGGTACTTAAACTTAACACTTTTTCTTAAG
* * *
13374 TTGATACCTAAACTTGACACTTTTT-TTAAG
1 TTGGTACTTAAACTTAACACTTTTTCTTAAG
13404 TTGGTACTTAAACTT
1 TTGGTACTTAAACTT
13419 TTTGGGGTCC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 17 0.45
31 21 0.55
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.45
Consensus pattern (31 bp):
TTGGTACTTAAACTTAACACTTTTTCTTAAG
Found at i:13434 original size:89 final size:90
Alignment explanation
Indices: 13297--13473 Score: 214
Period size: 89 Copynumber: 2.0 Consensus size: 90
13287 GTATCTGAAT
* ** * *
13297 TTGACACATTTTCTTAATTTAGTACTTAAACTTTTTTTGATCTAATTTGGTA-CTCAAACTTAAC
1 TTGACACATTTTCTTAAGTTAGTACTTAAACTTTTTGGGATCCAATTTGATACCT-AAACTTAAC
* **
13361 ACTTTTTCTTAATTTGATACCTAAAC
65 ACTATTTCCCAATTTGATACCTAAAC
* * * *
13387 TTGACAC-TTTTTTTAAGTTGGTACTTAAACTTTTTGGGGTCCAATTTGATACCTAAACTTAACT
1 TTGACACATTTTCTTAAGTTAGTACTTAAACTTTTTGGGATCCAATTTGATACCTAAACTTAACA
*
13451 CTATTTCCCAATTTGGTACCTAA
66 CTATTTCCCAATTTGATACCTAA
13474 TCTTTTTTTA
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
89 64 0.88
90 9 0.12
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.45
Consensus pattern (90 bp):
TTGACACATTTTCTTAAGTTAGTACTTAAACTTTTTGGGATCCAATTTGATACCTAAACTTAACA
CTATTTCCCAATTTGATACCTAAAC
Found at i:13749 original size:59 final size:58
Alignment explanation
Indices: 13615--13788 Score: 178
Period size: 59 Copynumber: 3.0 Consensus size: 58
13605 TAATATTTAA
13615 TAAA-TTTAG-TACCAAATTGAATCTAAAAAAAAAGTTTAGGTACCAAATTAGGAAAAA-TG
1 TAAAGTTTAGATACCAAATTGAATC--AAAAAAAA-TTTAGGTACCAAATTA-GAAAAATTG
* * ** *
13674 TCAAGTTCA-AGTACCAAATTGGGTCAAAAAAAATTTAGGTCCCAAATTAGAAGAAATTG
1 TAAAGTTTAGA-TACCAAATTGAATCAAAAAAAATTTAGGTACCAAATTAGAA-AAATTG
* * * *
13733 TAAAGTTTAGATACCAAATTGATTTAAAAAAAA-TTAGATACCAAATTAAAAAAATT
1 TAAAGTTTAGATACCAAATTGAATCAAAAAAAATTTAGGTACCAAATTAGAAAAATT
13789 ATCAAATTTA
Statistics
Matches: 96, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
57 8 0.08
58 33 0.34
59 39 0.41
60 4 0.04
61 12 0.12
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.28
Consensus pattern (58 bp):
TAAAGTTTAGATACCAAATTGAATCAAAAAAAATTTAGGTACCAAATTAGAAAAATTG
Found at i:18782 original size:60 final size:60
Alignment explanation
Indices: 18712--18848 Score: 175
Period size: 60 Copynumber: 2.3 Consensus size: 60
18702 TTAATATAAC
* * * * * * * *
18712 ATTTGGTACTTGAATTTGATATTTTTTCTTAATTTGGTACCTAAATATTTTTTGGACCTA
1 ATTTGGTACTTGAACTTGACACTTTTTCTTAATTTAGTACCTAAAAACTTTTTGAACCCA
* *
18772 ATTTGATACTTAAACTTGACACTTTTTCTTAATTTAGTACCTAAAAACTTTTTGAACCCA
1 ATTTGGTACTTGAACTTGACACTTTTTCTTAATTTAGTACCTAAAAACTTTTTGAACCCA
*
18832 ATTTGGTACATGAACTT
1 ATTTGGTACTTGAACTT
18849 CGCATTTTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (60 bp):
ATTTGGTACTTGAACTTGACACTTTTTCTTAATTTAGTACCTAAAAACTTTTTGAACCCA
Found at i:19212 original size:90 final size:90
Alignment explanation
Indices: 19047--19230 Score: 244
Period size: 90 Copynumber: 2.0 Consensus size: 90
19037 TTAAAAAAAA
* *
19047 TTAGGTATCAAATTAGGAAAAAGAGTCAAATTCAGGTACCAAATTGGATCATAAAAAGTTTAAGT
1 TTAGGTACCAAATTAGGAAAAAGAGTCAAATTCAGGTACCAAATTGGATCAAAAAAAGTTTAAGT
* *
19112 ACCAACTTAAAAAAAAGTGTCAAGC
66 ACCAAATTAAAAAAAAATGTCAAGC
* * * * * *
19137 TTAGGTACCAAATTAGGAAAGAGTGTCAAGTT-TGAGTATCAAATTGGATCAAAAAAAGTTTAGG
1 TTAGGTACCAAATTAGGAAAAAGAGTCAAATTCAG-GTACCAAATTGGATCAAAAAAAGTTTAAG
* *
19201 TATCAAATTAAAAAAAAATGTCAAGT
65 TACCAAATTAAAAAAAAATGTCAAGC
19227 TTAG
1 TTAG
19231 ATATCAAAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
89 1 0.01
90 80 0.99
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.27
Consensus pattern (90 bp):
TTAGGTACCAAATTAGGAAAAAGAGTCAAATTCAGGTACCAAATTGGATCAAAAAAAGTTTAAGT
ACCAAATTAAAAAAAAATGTCAAGC
Found at i:19230 original size:31 final size:31
Alignment explanation
Indices: 19102--19238 Score: 95
Period size: 31 Copynumber: 4.5 Consensus size: 31
19092 GGATCATAAA
* * * *
19102 AAGTTTAAGTACCAACTTAAAAAAAAGTGTC
1 AAGTTTAGGTATCAAATTAAAAAAAAATGTC
* * ** * *
19133 AAGCTTAGGTACCAAATTAGGAAAGAGTGTC
1 AAGTTTAGGTATCAAATTAAAAAAAAATGTC
* **
19164 AAGTTT-GAGTATCAAATTGGATCAAAAA----
1 AAGTTTAG-GTATCAAATT-AAAAAAAAATGTC
19192 AAGTTTAGGTATCAAATTAAAAAAAAATGTC
1 AAGTTTAGGTATCAAATTAAAAAAAAATGTC
*
19223 AAGTTTAGATATCAAA
1 AAGTTTAGGTATCAAA
19239 ATATTATATT
Statistics
Matches: 81, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
27 6 0.07
28 16 0.20
29 1 0.01
30 1 0.01
31 54 0.67
32 3 0.04
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.27
Consensus pattern (31 bp):
AAGTTTAGGTATCAAATTAAAAAAAAATGTC
Found at i:19736 original size:2 final size:2
Alignment explanation
Indices: 19723--19769 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
19713 AAGCAAAAGC
* *
19723 GA GA GA GC GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
19765 GA GA G
1 GA GA G
19770 CAAAAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:25572 original size:18 final size:18
Alignment explanation
Indices: 25540--25591 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
25530 TTGAGATGAG
25540 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
25556 AATAAATTTAATTAATTA
1 AATAAATTTAATTAATTA
*
25574 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
25592 CAACTGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 9 0.28
17 5 0.16
18 18 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:25742 original size:20 final size:20
Alignment explanation
Indices: 25708--25745 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25698 TGATCACTTT
25708 GTAACAAAACGATAATATAA
1 GTAACAAAACGATAATATAA
25728 GTAACTAAAAC-ATAATAT
1 GTAAC-AAAACGATAATAT
25746 TTCAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.58, C:0.11, G:0.08, T:0.24
Consensus pattern (20 bp):
GTAACAAAACGATAATATAA
Found at i:25759 original size:15 final size:15
Alignment explanation
Indices: 25721--25771 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
25711 ACAAAACGAT
* *
25721 AATATAAGTAACTAA
1 AATATAAATAATTAA
* * *
25736 AACAT-AATATTTCA
1 AATATAAATAATTAA
25750 AATATAAATAATTAA
1 AATATAAATAATTAA
25765 AATATAA
1 AATATAA
25772 TTTAAAATAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (15 bp):
AATATAAATAATTAA
Found at i:26651 original size:27 final size:26
Alignment explanation
Indices: 26621--26681 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
26611 TCAGATTTCG
* *
26621 AGTTTGGATTTTGGGTTTGAGATTTAA
1 AGTTTGGATTTT-AGTTTAAGATTTAA
*
26648 AGTTTAGGGTTTTAGTTTAAGATTTAA
1 AGTTT-GGATTTTAGTTTAAGATTTAA
26675 AGGTTTG
1 A-GTTTG
26682 AGGTTATGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.48
Consensus pattern (26 bp):
AGTTTGGATTTTAGTTTAAGATTTAA
Found at i:28729 original size:64 final size:64
Alignment explanation
Indices: 28628--28755 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
28618 CATGTAGCAA
28628 TTGTTTACACTAAGAGGATGTTTGATACCATGGGAAGTTTCAACTTTTCAATATATTTAATTGG
1 TTGTTTACACTAAGAGGATGTTTGATACCATGGGAAGTTTCAACTTTTCAATATATTTAATTGG
**
28692 TTGTTTACACTAAGAGGATGTTTGATAGTATGGGAAGTTTCAACTTTTCAATATATTTAATTGG
1 TTGTTTACACTAAGAGGATGTTTGATACCATGGGAAGTTTCAACTTTTCAATATATTTAATTGG
28756 CTGAAATGTG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (64 bp):
TTGTTTACACTAAGAGGATGTTTGATACCATGGGAAGTTTCAACTTTTCAATATATTTAATTGG
Done.