Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013043.1 Kokia drynarioides strain JFW-HI SEQ_128061, 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: 13403
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:3726 original size:29 final size:29
Alignment explanation
Indices: 3663--3859 Score: 135
Period size: 29 Copynumber: 6.7 Consensus size: 29
3653 TAAACTGTCC
3663 AAAAATTATATTTTGACCCTCTAAC-TTCTT
1 AAAAATTATATTTTGACCC-CTAACTTTC-T
* *
3693 TAAAATTATATTTTTGA-CTCTAACTTTCT
1 AAAAATTATA-TTTTGACCCCTAACTTTCT
*
3722 AAAAATTACATTTT-ACCCCTAAACTTATCT
1 AAAAATTATATTTTGACCCCT-AACTT-TCT
*
3752 -AAAATTATATTTTG-GCCCTAACTTTTCT
1 AAAAATTATATTTTGACCCCTAAC-TTTCT
*
3780 AAAAATTACATTTAT-ACCCCTAAAACTTT-T
1 AAAAATTATATTT-TGACCCCT--AACTTTCT
* **
3810 CAAAAATTCTATTTTTGACCTCAAAACTTTC-
1 -AAAAATTATA-TTTTGACC-CCTAACTTTCT
3841 -AAAATTATCATTTT-ACCCC
1 AAAAATTAT-ATTTTGACCCC
3860 CGGATGTCCA
Statistics
Matches: 134, Mismatches: 15, Indels: 39
0.71 0.08 0.21
Matches are distributed among these distances:
27 2 0.01
28 16 0.12
29 59 0.44
30 23 0.17
31 24 0.18
32 9 0.07
33 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.42
Consensus pattern (29 bp):
AAAAATTATATTTTGACCCCTAACTTTCT
Found at i:3758 original size:58 final size:58
Alignment explanation
Indices: 3663--3859 Score: 213
Period size: 58 Copynumber: 3.3 Consensus size: 58
3653 TAAACTGTCC
* * *
3663 AAAAATTATATTTTGACCCTCT-AACTTCTTTAAAATTATATTTTTGACTCTAACTTTCT
1 AAAAATTACATTTT-ACCC-CTAAACTTATCTAAAATTATATTTTTGACTCTAACTTTCT
* *
3722 AAAAATTACATTTTACCCCTAAACTTATCTAAAATTATA-TTTTGGCCCTAACTTTTCT
1 AAAAATTACATTTTACCCCTAAACTTATCTAAAATTATATTTTTGACTCTAAC-TTTCT
* * * *
3780 AAAAATTACATTTATACCCCTAAAACTTTTCAAAAATTCTATTTTTGACCTCAAAACTTTC-
1 AAAAATTACATTT-TACCCCT-AAACTTATCTAAAATTATATTTTTGA-CTC-TAACTTTCT
3841 -AAAATTATCATTTTACCCC
1 AAAAATTA-CATTTTACCCC
3860 CGGATGTCCA
Statistics
Matches: 119, Mismatches: 11, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
57 13 0.11
58 38 0.32
59 20 0.17
60 29 0.24
61 10 0.08
62 6 0.05
63 3 0.03
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.42
Consensus pattern (58 bp):
AAAAATTACATTTTACCCCTAAACTTATCTAAAATTATATTTTTGACTCTAACTTTCT
Found at i:3906 original size:60 final size:59
Alignment explanation
Indices: 3821--4006 Score: 203
Period size: 59 Copynumber: 3.2 Consensus size: 59
3811 AAAAATTCTA
* * * *
3821 TTTTTGACCTCAAAACTTTC-AAAATTATCATTTTACCCCCGGATGTCCAAAAATTCCG
1 TTTTTGATCTCGAAACTTTCAAAAATTATCATTTTACCCTCGGATGTCCAAAAATTTCG
**** *** * * *
3879 TTTTTGATCTCTGTTTTTTTTTTAAATTATCGTTTTACCCTCGGATGTCTAAAAATTTCA
1 TTTTTGATCTC-GAAACTTTCAAAAATTATCATTTTACCCTCGGATGTCCAAAAATTTCG
* * *
3939 TTTTTGACCTCGAAACTTTCAAAAATTACCATTTTACCCTCAGATGTCCAAAAATTTCG
1 TTTTTGATCTCGAAACTTTCAAAAATTATCATTTTACCCTCGGATGTCCAAAAATTTCG
3998 TTTTTGATC
1 TTTTTGATC
4007 CCAATTTTTC
Statistics
Matches: 99, Mismatches: 27, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
58 10 0.10
59 47 0.47
60 42 0.42
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.42
Consensus pattern (59 bp):
TTTTTGATCTCGAAACTTTCAAAAATTATCATTTTACCCTCGGATGTCCAAAAATTTCG
Found at i:3943 original size:29 final size:28
Alignment explanation
Indices: 3911--4002 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 28
3901 TAAATTATCG
3911 TTTTACCCTCGGATGTCTAAAAATTTCAT
1 TTTTACCCTCGGATGTC-AAAAATTTCAT
* * *
3940 TTTTGA-CCTCGAAACTTTCAAAAATTACCA-
1 TTTT-ACCCTCG-GA-TGTCAAAAATT-TCAT
* *
3970 TTTTACCCTCAGATGTCCAAAAATTTCGT
1 TTTTACCCTCGGATGT-CAAAAATTTCAT
3999 TTTT
1 TTTT
4003 GATCCCAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
28 3 0.06
29 23 0.48
30 17 0.35
31 5 0.10
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (28 bp):
TTTTACCCTCGGATGTCAAAAATTTCAT
Found at i:3986 original size:59 final size:58
Alignment explanation
Indices: 3810--4004 Score: 203
Period size: 60 Copynumber: 3.3 Consensus size: 58
3800 TAAAACTTTT
* *
3810 CAAAAA-TTCTATTTTTGACCTCAAAACTTTCAAAATTATCATTTTACCCCCGGATGTC
1 CAAAAATTTC-ATTTTTGACCTCGAAACTTTCAAAATTATCATTTTACCCTCGGATGTC
* * * **** ** *
3868 CAAAAATTCCGTTTTTGATCTCTGTTTTTTTTTTAAATTATCGTTTTACCCTCGGATGTC
1 CAAAAATTTCATTTTTGACCTC-G-AAACTTTCAAAATTATCATTTTACCCTCGGATGTC
* * *
3928 TAAAAATTTCATTTTTGACCTCGAAACTTTCAAAAATTACCATTTTACCCTCAGATGTC
1 CAAAAATTTCATTTTTGACCTCGAAACTTTC-AAAATTATCATTTTACCCTCGGATGTC
*
3987 CAAAAATTTCGTTTTTGA
1 CAAAAATTTCATTTTTGA
4005 TCCCAATTTT
Statistics
Matches: 106, Mismatches: 27, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
58 19 0.18
59 42 0.40
60 45 0.42
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.42
Consensus pattern (58 bp):
CAAAAATTTCATTTTTGACCTCGAAACTTTCAAAATTATCATTTTACCCTCGGATGTC
Found at i:4022 original size:59 final size:59
Alignment explanation
Indices: 3841--4032 Score: 190
Period size: 59 Copynumber: 3.2 Consensus size: 59
3831 CAAAACTTTC
* * * *** * *
3841 AAAATTATCATTTTACCCCCGGATGTCCAAAAATTCCGTTTTTGATCTCTGTTTTTTTTT
1 AAAATTACCATTTTACCCTCGGATGTCCAAAAATTTCGTTTTTGATC-CCAATTTTTCTA
* * * * * **
3901 TAAATTATCGTTTTACCCTCGGATGTCTAAAAATTTCATTTTTGA-CCTCGAAACTTTC-A
1 AAAATTACCATTTTACCCTCGGATGTCCAAAAATTTCGTTTTTGATCC-C-AATTTTTCTA
*
3960 AAAATTACCATTTTACCCTCAGATGTCCAAAAATTTCGTTTTTGATCCCAATTTTTCTA
1 AAAATTACCATTTTACCCTCGGATGTCCAAAAATTTCGTTTTTGATCCCAATTTTTCTA
*
4019 AAAATTACCGTTTT
1 AAAATTACCATTTT
4033 TGCCCCTCCA
Statistics
Matches: 106, Mismatches: 22, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
58 7 0.07
59 55 0.52
60 44 0.42
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (59 bp):
AAAATTACCATTTTACCCTCGGATGTCCAAAAATTTCGTTTTTGATCCCAATTTTTCTA
Found at i:4060 original size:22 final size:23
Alignment explanation
Indices: 4019--4061 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
4009 AATTTTTCTA
* *
4019 AAAATTACCGTTTTTGCCCCTCC
1 AAAATTACCGATTTTACCCCTCC
4042 AAAATTACC-ATTTTACCCCT
1 AAAATTACCGATTTTACCCCT
4062 TGAGTATCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.28, C:0.33, G:0.05, T:0.35
Consensus pattern (23 bp):
AAAATTACCGATTTTACCCCTCC
Found at i:7624 original size:33 final size:33
Alignment explanation
Indices: 7587--7652 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
7577 ATCTGTGTAC
7587 ACTAACCTTCATAATGCAATAATTAGATTTTAA
1 ACTAACCTTCATAATGCAATAATTAGATTTTAA
7620 ACTAACCTTCATAATGCAATAATTAGATTTTAA
1 ACTAACCTTCATAATGCAATAATTAGATTTTAA
7653 GCACAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (33 bp):
ACTAACCTTCATAATGCAATAATTAGATTTTAA
Found at i:10216 original size:40 final size:39
Alignment explanation
Indices: 10172--10314 Score: 153
Period size: 40 Copynumber: 3.6 Consensus size: 39
10162 AGCATTGCAA
* * * *
10172 TGTTTACAGTGTCACTGCCTGCTT-AGTTATAATATCGTAG
1 TGTTTACAATGTCACTGCCAG-TTCAG-TAAAACATCGTAG
* * **
10212 TGTTTTCAATGTCACTGTCAGTTCAGTAAAGACATCACAG
1 TGTTTACAATGTCACTGCCAGTTCAGTAAA-ACATCGTAG
10252 TGTTTACAATGTCACTGCCAGTTCAGTAAAGACATCGTAG
1 TGTTTACAATGTCACTGCCAGTTCAGTAAA-ACATCGTAG
* *
10292 TGTTTACAGTGTCACTGCTAGTT
1 TGTTTACAATGTCACTGCCAGTT
10315 TAAACATTTT
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 5 0.06
40 82 0.94
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (39 bp):
TGTTTACAATGTCACTGCCAGTTCAGTAAAACATCGTAG
Found at i:10256 original size:80 final size:81
Alignment explanation
Indices: 10088--10314 Score: 223
Period size: 80 Copynumber: 2.8 Consensus size: 81
10078 AATAAGCTAG
* *
10088 CAGTGTTTACAGTGTCACTTG-CTAGTCCAGTTGCAATATCGTAGTGTTTACAATGTCACTGCCG
1 CAGTGTTTACAGTGTCAC-TGCCTAGTCCAGTTACAATATCGTAGTGTTTACAATGTCACTGCCA
* **
10152 GTTCAATGATAGCATTG
65 GTTCAATGAAAGCATCA
* * * * *
10169 CAATGTTTACAGTGTCACTGCCT-G-CTTAGTTATAATATCGTAGTGTTTTCAATGTCACTGTCA
1 CAGTGTTTACAGTGTCACTGCCTAGTC-CAGTTACAATATCGTAGTGTTTACAATGTCACTGCCA
*
10232 GTTCAGT-AAAGACATCA
65 GTTCAATGAAAG-CATCA
* * * * * *
10249 CAGTGTTTACAATGTCACTGCC-AGTTCAG-TAAAGACATCGTAGTGTTTACAGTGTCACTGCTA
1 CAGTGTTTACAGTGTCACTGCCTAGTCCAGTTACA-ATATCGTAGTGTTTACAATGTCACTGCCA
10312 GTT
65 GTT
10315 TAAACATTTT
Statistics
Matches: 119, Mismatches: 21, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
79 7 0.06
80 93 0.78
81 19 0.16
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (81 bp):
CAGTGTTTACAGTGTCACTGCCTAGTCCAGTTACAATATCGTAGTGTTTACAATGTCACTGCCAG
TTCAATGAAAGCATCA
Done.