Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011670.1 Kokia drynarioides strain JFW-HI SEQ_126662, 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: 18133
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Warning! 98 characters in sequence are not A, C, G, or T
Found at i:6788 original size:2 final size:2
Alignment explanation
Indices: 6781--6818 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
6771 TTATTAACTA
6781 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
6819 AAAGAATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10580 original size:14 final size:14
Alignment explanation
Indices: 10561--10596 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
10551 TTGTTTTATT
*
10561 GAAAATGATTTTTG
1 GAAAATGATTTCTG
10575 GAAAATGATTTCTG
1 GAAAATGATTTCTG
*
10589 AAAAATGA
1 GAAAATGA
10597 CTTACTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.33
Consensus pattern (14 bp):
GAAAATGATTTCTG
Found at i:11084 original size:15 final size:15
Alignment explanation
Indices: 11064--11115 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
11054 ACTACAAAAC
11064 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
11079 ATTTATAAATGTAATAAAT
1 ATTTAT-TAT-TAAT--AT
*
11098 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
11113 ATT
1 ATT
11116 AATGTTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 11 0.37
16 2 0.07
17 7 0.23
18 2 0.07
19 8 0.27
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:12360 original size:24 final size:24
Alignment explanation
Indices: 12291--12365 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
12281 TCAGTTAAAT
* * *
12291 TCTGTTTATTTATTTAAATTAAAT
1 TCTGTTTATTTGTTTAAATCAAAC
* * * *
12315 TTTATTTATTTGTTTGAGTCAAAC
1 TCTGTTTATTTGTTTAAATCAAAC
12339 TCTGTTTATTTGTTTAAATCAAAC
1 TCTGTTTATTTGTTTAAATCAAAC
12363 TCT
1 TCT
12366 TATTAGTCTA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.28, C:0.09, G:0.08, T:0.55
Consensus pattern (24 bp):
TCTGTTTATTTGTTTAAATCAAAC
Found at i:12742 original size:6 final size:6
Alignment explanation
Indices: 12731--12813 Score: 59
Period size: 6 Copynumber: 14.5 Consensus size: 6
12721 GGCCCAACAG
* * * *
12731 AATTTA AATTT- ATTTTA AAATTA AATTT- ATTTTA AGTTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * *
12776 ACTTAA AATTTA AATTT- -ATTATA AATTTA AGTTTA AAT
1 AATTTA AATTTA AATTTA AATT-TA AATTTA AATTTA AAT
12814 CTATTTAAAT
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
4 3 0.05
5 12 0.21
6 40 0.69
7 3 0.05
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:12756 original size:17 final size:17
Alignment explanation
Indices: 12734--12810 Score: 84
Period size: 17 Copynumber: 4.5 Consensus size: 17
12724 CCAACAGAAT
12734 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
**
12751 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAA
*
12768 TTAAATTTA-CTTAAAA
1 TTAAATTTATTTTAAAA
* *
12784 TTTAAATTTATTATAAAT
1 -TTAAATTTATTTTAAAA
*
12802 TTAAGTTTA
1 TTAAATTTA
12811 AATCTATTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
16 4 0.08
17 41 0.84
18 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:12758 original size:23 final size:23
Alignment explanation
Indices: 12731--12819 Score: 63
Period size: 23 Copynumber: 3.7 Consensus size: 23
12721 GGCCCAACAG
12731 AATTTAAATTTATTTTAAAATTA
1 AATTTAAATTTATTTTAAAATTA
* *
12754 AATTT-ATTTTAAGTTTAAATTTACTTAA
1 AATTTAAATTT-ATTTTAAA---A-TT-A
* *
12782 AATTTAAATTTATTATAAATTTA
1 AATTTAAATTTATTTTAAAATTA
* *
12805 AGTTTAAATCTATTT
1 AATTTAAATTTATTT
12820 AAATCAAAGG
Statistics
Matches: 50, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
22 4 0.08
23 25 0.50
24 2 0.04
26 1 0.02
27 2 0.04
28 12 0.24
29 4 0.08
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
AATTTAAATTTATTTTAAAATTA
Found at i:12776 original size:34 final size:34
Alignment explanation
Indices: 12731--12810 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 34
12721 GGCCCAACAG
* *
12731 AATTTAAATTTATTTTAAAA-TTAAATTTATTTTA
1 AATTTAAATTTA-CTTAAAATTTAAATTTATTATA
*
12765 AGTTTAAATTTACTTAAAATTTAAATTTATTATA
1 AATTTAAATTTACTTAAAATTTAAATTTATTATA
*
12799 AATTTAAGTTTA
1 AATTTAAATTTA
12811 AATCTATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 6 0.15
34 34 0.85
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
AATTTAAATTTACTTAAAATTTAAATTTATTATA
Found at i:13642 original size:22 final size:22
Alignment explanation
Indices: 13617--13667 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
13607 CATATTAAAC
13617 ATATTAAATAATTTTATTAATG
1 ATATTAAATAATTTTATTAATG
*
13639 ATATTGAATAATTTTATTAATG
1 ATATTAAATAATTTTATTAATG
13661 ATATTAA
1 ATATTAA
13668 TAAGGCTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (22 bp):
ATATTAAATAATTTTATTAATG
Found at i:13693 original size:14 final size:14
Alignment explanation
Indices: 13676--13712 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
13666 AATAAGGCTT
13676 TAATAATATAATAA
1 TAATAATATAATAA
*
13690 TAATAATA-AATAG
1 TAATAATATAATAA
13703 TAATAA-ATAA
1 TAATAATATAA
13713 AAAAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 1 0.05
13 12 0.57
14 8 0.38
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
TAATAATATAATAA
Found at i:14781 original size:29 final size:30
Alignment explanation
Indices: 14732--14991 Score: 214
Period size: 29 Copynumber: 8.7 Consensus size: 30
14722 GAGGTCCATA
**
14732 AACTATTCAAAAATTATATTTTT-ACCCTCG
1 AACT-TTCAAAAATTCCATTTTTGACCCTCG
* **
14762 AACTTTCAAAAATTCCATTTTTGACCTTAA
1 AACTTTCAAAAATTCCATTTTTGACCCTCG
* *
14792 AACTTCCAAAAATTCCATTTTTGACCC-CAA
1 AACTTTCAAAAATTCCATTTTTGACCCTC-G
* **
14822 AACTTCCAAAAATTCCA-TTTCAACCC-CG
1 AACTTTCAAAAATTCCATTTTTGACCCTCG
*
14850 TAACTTCCAAAAATTCCATTTTT-ACCCTCG
1 -AACTTTCAAAAATTCCATTTTTGACCCTCG
* * * *
14880 AACTTCCAAAAATTCAATTTTTGA-TCTCAA
1 AACTTTCAAAAATTCCATTTTTGACCCTC-G
* *
14910 AACTTTCAAAAATTCCATGTTT-ACCCCCG
1 AACTTTCAAAAATTCCATTTTTGACCCTCG
* *
14939 AAC-CTCTAAAATTTCCATTTTTGA-CCTCG
1 AACTTTC-AAAAATTCCATTTTTGACCCTCG
*
14968 AAGCTTTCAAAAATTATCATTTTT
1 AA-CTTTCAAAAATT-CCATTTTT
14992 CCCCCGGATG
Statistics
Matches: 189, Mismatches: 28, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.01
29 92 0.49
30 86 0.46
31 9 0.05
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (30 bp):
AACTTTCAAAAATTCCATTTTTGACCCTCG
Found at i:14802 original size:30 final size:30
Alignment explanation
Indices: 14762--14991 Score: 207
Period size: 30 Copynumber: 7.7 Consensus size: 30
14752 TTTACCCTCG
* **
14762 AACTTTCAAAAATTCCATTTTTGACCTTAA
1 AACTTCCAAAAATTCCATTTTTGACCCCAA
14792 AACTTCCAAAAATTCCATTTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTTGACCCCAA
** **
14822 AACTTCCAAAAATTCCA-TTTCAACCCCGT
1 AACTTCCAAAAATTCCATTTTTGACCCCAA
*
14851 AACTTCCAAAAATTCCATTTTT-ACCCTC-G
1 AACTTCCAAAAATTCCATTTTTGACCC-CAA
* * *
14880 AACTTCCAAAAATTCAATTTTTGATCTCAA
1 AACTTCCAAAAATTCCATTTTTGACCCCAA
* * **
14910 AACTTTCAAAAATTCCATGTTT-ACCCCCG
1 AACTTCCAAAAATTCCATTTTTGACCCCAA
* * * * *
14939 AACCTCTAAAATTTCCATTTTTGACCTCGA
1 AACTTCCAAAAATTCCATTTTTGACCCCAA
* * *
14969 AGCTTTCAAAAATTATCATTTTT
1 AACTTCCAAAAATT-CCATTTTT
14992 CCCCCGGATG
Statistics
Matches: 160, Mismatches: 34, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
29 71 0.44
30 82 0.51
31 7 0.04
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.35
Consensus pattern (30 bp):
AACTTCCAAAAATTCCATTTTTGACCCCAA
Found at i:14979 original size:118 final size:117
Alignment explanation
Indices: 14732--15107 Score: 370
Period size: 118 Copynumber: 3.2 Consensus size: 117
14722 GAGGTCCATA
* * *
14732 AACTATTCAAAAATTA-TATTTTTACCCTCGAACTTTCAAAAATTCCATTTTTGACCTTAAAACT
1 AACT-TTCAAAAATTACCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCAAAACT
* ** * * *
14796 TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCA-TTTCAACCCCG
65 TTCAAAAATTCCA-TTTT-ACCCCCGAACATCTAAAAATTCCATTTTTAACCCCG
* * *
14850 TAACTTCCAAAAATT-CCATTTTTACCCTCGAACTTCCAAAAATTCAATTTTTGATCTCAAAACT
1 -AACTTTCAAAAATTACCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCAAAACT
* * * *
14914 TTCAAAAATTCCATGTTTACCCCCGAACCTCTAAAATTTCCATTTTTGACCTCG
65 TTCAAAAATTCCAT-TTTACCCCCGAACATCTAAAAATTCCATTTTTAACCCCG
* * * * * *
14968 AAGCTTTCAAAAATTATCATTTTT-CCCCCGGA-TGTCCAGAAACTCCATTTTCT-ACCTGAAAA
1 AA-CTTTCAAAAATTACCATTTTTACCCTCGAACT-TCCAAAAATTCCATTTT-TGACCTCAAAA
* * * *
15030 CTCTC-AAAATTACCCTTTTACCGCCGAATATCTAAAAATTCCATTTTTAACCCCG
63 CTTTCAAAAATT-CCATTTTACCCCCGAACATCTAAAAATTCCATTTTTAACCCCG
*
15085 AACTTTCCCAAAATTACCATTTT
1 AACTTT-CAAAAATTACCATTTT
15108 GCCCCTCGGG
Statistics
Matches: 214, Mismatches: 34, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
116 4 0.02
117 78 0.36
118 120 0.56
119 12 0.06
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (117 bp):
AACTTTCAAAAATTACCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCAAAACTT
TCAAAAATTCCATTTTACCCCCGAACATCTAAAAATTCCATTTTTAACCCCG
Found at i:14996 original size:59 final size:59
Alignment explanation
Indices: 14731--15077 Score: 272
Period size: 59 Copynumber: 5.9 Consensus size: 59
14721 GGAGGTCCAT
** * * * *
14731 AAACTATTCAAAAATTATATTTTTACCCTCGAACTTTCAAAAATTCCATTTTTGACCTTA
1 AAACT-TTCAAAAATTCCATTTTTACCCCCGAACCTCCAAAAATTCCATTTTTGACCTCA
* ** * ** * *
14791 AAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCA-TTTCAACCCCG
1 AAACTTTCAAAAATTCCATTTTT-ACCCCCGAACCTCCAAAAATTCCATTTTTGACCTCA
* * * * * *
14850 TAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCAATTTTTGATCTCA
1 AAACTTTCAAAAATTCCATTTTTACCCCCGAACCTCCAAAAATTCCATTTTTGACCTCA
* * * *
14909 AAACTTTCAAAAATTCCATGTTTACCCCCGAACCTCTAAAATTTCCATTTTTGACCTCG
1 AAACTTTCAAAAATTCCATTTTTACCCCCGAACCTCCAAAAATTCCATTTTTGACCTCA
* * * ** * * *
14968 AAGCTTTCAAAAATTATCATTTTT-CCCCCGGATGTCCAGAAACTCCATTTTCT-ACCTGA
1 AAACTTTCAAAAATT-CCATTTTTACCCCCGAACCTCCAAAAATTCCATTTT-TGACCTCA
* * * ** *
15027 AAACTCTC-AAAATTACC-CTTTTACCGCCGAATATCTAAAAATTCCATTTTT
1 AAACTTTCAAAAATT-CCATTTTTACCCCCGAACCTCCAAAAATTCCATTTTT
15078 AACCCCGAAC
Statistics
Matches: 228, Mismatches: 54, Indels: 13
0.77 0.18 0.04
Matches are distributed among these distances:
57 5 0.02
58 49 0.21
59 142 0.62
60 32 0.14
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.35
Consensus pattern (59 bp):
AAACTTTCAAAAATTCCATTTTTACCCCCGAACCTCCAAAAATTCCATTTTTGACCTCA
Done.