Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007743.1 Kokia drynarioides strain JFW-HI SEQ_122376, 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: 5563
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2694 original size:20 final size:22
Alignment explanation
Indices: 2650--2702 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 22
2640 ATATTTTTTG
*
2650 TTTTTCT-TTTCTTCTTTGTCC
1 TTTTTCTCTTTGTTCTTTGTCC
2671 -TTTTCTCTTTGTT-TTT-TCC
1 TTTTTCTCTTTGTTCTTTGTCC
*
2690 TTTTTGTCTTTGT
1 TTTTTCTCTTTGT
2703 GCTTCTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 3 0.11
20 20 0.71
21 5 0.18
ACGTcount: A:0.00, C:0.19, G:0.08, T:0.74
Consensus pattern (22 bp):
TTTTTCTCTTTGTTCTTTGTCC
Found at i:3531 original size:41 final size:42
Alignment explanation
Indices: 3474--3609 Score: 129
Period size: 41 Copynumber: 3.4 Consensus size: 42
3464 TCTTGGTTTA
* ** * *
3474 GGGGTAAAAGATTGGATGGTGGCTTTAACCTGTCCCA-TATC
1 GGGGTAAGAGATTGGATGGCAGCTTCAACCTGCCCCATTATC
* * *
3515 GGGGTAAGAGATTGGATGACATCTTCAATCTGCCCCATTATC
1 GGGGTAAGAGATTGGATGGCAGCTTCAACCTGCCCCATTATC
* *
3557 -GGGTAAGAGATTGGAT-G--GCTTCAACCTGCCCCGTGATC
1 GGGGTAAGAGATTGGATGGCAGCTTCAACCTGCCCCATTATC
* *
3595 AGGGTAAAAGATTGG
1 GGGGTAAGAGATTGG
3610 TGTGTTTTCA
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
38 17 0.22
39 13 0.16
41 45 0.57
42 4 0.05
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (42 bp):
GGGGTAAGAGATTGGATGGCAGCTTCAACCTGCCCCATTATC
Found at i:4227 original size:39 final size:37
Alignment explanation
Indices: 3507--5175 Score: 371
Period size: 38 Copynumber: 42.6 Consensus size: 37
3497 TTTAACCTGT
*
3507 CCCAT-ATCGGGGTAAGAGATTGGATGACATCTTCAATCTG
1 CCCATGATCGGGGTAAGAGATTGGA-G--GT-TTCAATCTG
* * *
3547 CCCCATTATC-GGGTAAGAGATTGGATGGCTTCAACCTG
1 -CCCATGATCGGGGTAAGAGATTGGA-GGTTTCAATCTG
* * * * *
3585 CCCCGTGATCAGGGTAAAAGATTGGTGTGTTTTCAATCTAA
1 -CCCATGATCGGGGTAAGAGATTGGAG-G-TTTCAATCT-G
* ** * **
3626 CCCTCTGATTAGGGTAAAAGATT-GAATTCTTCAATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGAGGT-TTCAATCTG
* * * *
3664 CCCCATAATCGGGGTAAGAGATTGGTGTCTCTTCAAT-TT
1 -CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* *** * * * *
3703 CCCTCTGATTATGATAAAAGATCGGATGTTTCAATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
** * *
3741 CCTCATGATCAAGGTAAGAGATTGGTGTGTCTTCAATCTA
1 CC-CATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* ** * * ** *
3781 CCCTCTGATTAGGGTAAAATATCAGATGG-TTCAATATG
1 CCC-ATGATCGGGGTAAGAGATTGGA-GGTTTCAATCTG
* * ** *
3819 TCCCATGATCAGGGCAAGAGATTAATATGTCTTCAATCTG
1 -CCCATGATCGGGGTAAGAGATT-GGAGGT-TTCAATCTG
** * * * * * *
3859 CGCTC-TGATTAGGGTAAAAGATCGAATGCTTCTATCTG
1 C-C-CATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
* * * * *
3897 TACCATGATCGGGATAAGAGATTGGTGTATCTTCAATCTA
1 -CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* ** * * * *
3937 CCCTTTGATTAGGGTAAAAGATCGGATGCTTCAATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
* * * *
3975 CCTCATGATTGGGGTAAGAGATTAGTGTGTCTTCAATCTA
1 CC-CATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* ** * * * * * *
4015 CCCTCTGATTAGGGTAAAAGATCGAATGCTTCTATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
* * * *
4053 CCCCATGATTGGGGTAAGAGATTGGTGTGTCTTTAATTTG
1 -CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* * ** **
4093 CCCTCTAATTAGGGTAAGAGATTGGATATTTCAATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
4131 CCCCATGATCGGGGTAAGAGATTGGATGATGTTTACAATCTG
1 -CCCATGATCGGGGTAAGAGATTGGA-G--GTTT-CAATCTG
* * **
4173 CCCTCTAATTAGGGTAAGAGATTGGACGGTTGT-AATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGA-GGTT-TCAATCTG
* *
4212 TCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTA
1 -CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* ** * ** * *
4252 CCCTCTGATTAGGGTAAAAGATCAGATGCTTCAATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
4290 TCCCATGATCGGGGTAAGAGATTGGAGTGTCTTCAATCTG
1 -CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* * ** * * * *
4330 CCCTCTAATTAGGGTAAAAGATCGGATGCTTCAATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
* * * *
4368 CCTCATGATTGGGGTAAAAGATTGAATGTCTTCAATCTG
1 CC-CATGATCGGGGTAAGAGATTGGAGGT-TTCAATCTG
* * ** * **
4407 CCCTCTAATTAGGGTAAAAGATTGGTTGTTTCAATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
* * *
4445 CCTCGTGATCGGGGTAAGAGATTGGATGATGTTTTCAATTTA
1 CC-CATGATCGGGGTAAGAGATTGGA-G--G-TTTCAATCTG
* * * *** * * *
4487 CCCTCTAATTGGGGTAAGAGATTGGACAACTACTATCTAT
1 CCC-ATGATCGGGGTAAGAGATTGGA-GGTTTCAATCT-G
* *
4527 CCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATATG
1 CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* ** * * *
4566 CCTTC-TAATTAGGGTAAAAGATTGGATGCTTCAATCTG
1 CC--CATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
* * ** * * *
4604 CCTCATAACCAAGGTAAAAGATT-GATGTGTCTTCTATTTG
1 CC-CATGATCGGGGTAAGAGATTGGA-G-GT-TTCAATCTG
* * * *
4644 CCCTCTGATTGGGGTAAGAGATTGGACGACTGT-AATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGA-G-GTTTCAATCTG
* * * *
4683 CCCCATGATCGGGGTAAGAGATTGGCGTGTCTTCTATTTT
1 -CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* * * * * * *
4723 CCCTTTGATTGGGTTAAGAGATTTGACGACTGT-AATTTG
1 CCC-ATGATCGGGGTAAGAGATTGGA-G-GTTTCAATCTG
* *
4762 CCCCATGATCAGGGTAAGAGATTGGTGTGTCTTCAATCTG
1 -CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
** * ** * * * * *
4802 CCTTC-TGATTAGGGTAAAAGATCAGATGCTTAAATTTTC
1 CC--CATGATCGGGGTAAGAGATTGGAGGTTTCAA-TCTG
* * *
4841 CCCATGATCGGGGTAAGTGATTGGTGTGTCTTCAATCTA
1 CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* ** * * * * *
4880 CCCTTTGATTAGGGTAAAAGATTGGATGCTTCAATTTAC
1 CCC-ATGATCGGGGTAAGAGATTGGAGGTTTCAATCT-G
* *
4919 CCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTAT
1 CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCT-G
** ** * * * *
4959 CCTTTGATTAGGGTAAAAGATCGGATGCTTCAATCTG
1 CCCATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
** *
4996 CCCCATGATCGGGGTAAGAGATTGTTGTGTCTTCAATCTA
1 -CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
*** * * *
5036 CCTTC-TGATTAAGGTAAAAGATTGGATGCTTCAATCTG
1 CC--CATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
*
5074 CCCCATGATCAGGGTAAGAGATT-GATGTGTCTTCAATCTG
1 -CCCATGATCGGGGTAAGAGATTGGA-G-GT-TTCAATCTG
*** * * *
5114 CCTTC-TGATTAAGGTAAAAGATTGGATGCTTCAATCTG
1 CC--CATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
5152 CCCCATGATCGGGGTAAGAGATTG
1 -CCCATGATCGGGGTAAGAGATTG
5176 AATGGTGATG
Statistics
Matches: 1159, Mismatches: 364, Indels: 213
0.67 0.21 0.12
Matches are distributed among these distances:
37 16 0.01
38 398 0.34
39 248 0.21
40 377 0.33
41 62 0.05
42 58 0.05
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (37 bp):
CCCATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
Found at i:5176 original size:78 final size:78
Alignment explanation
Indices: 3450--5175 Score: 1843
Period size: 78 Copynumber: 21.9 Consensus size: 78
3440 GAGATGATAA
* * * *
3450 CTTCAATCTGCCCCTCTTGGTTTAGGGGTAAAAGATTGGATGGTGGCTTTAACCTGTCCCAT-AT
1 CTTCAATCTG-CCCTC-T-GATTA-GGGTAAAAGATTGGA---T-GCTTCAATCTGCCCCATGAT
**
3514 CGGGGTAAGAGATTGGATGACAT
58 CGGGGTAAGAGATTGG-TG-TGT
* * * *
3537 CTTCAATCTGCCC-C--ATTATCGGGTAAGAGATTGGATGGCTTCAACCTGCCCCGTGATCAGGG
1 CTTCAATCTGCCCTCTGATTA--GGGTAAAAGATTGGAT-GCTTCAATCTGCCCCATGATCGGGG
*
3599 TAAAAGATTGGTGTGT
63 TAAGAGATTGGTGTGT
* * * * *
3615 TTTCAATCTAACCCTCTGATTAGGGTAAAAGATTGAATTCTTCAATCTGCCCCATAATCGGGGTA
1 CTTCAATCT-GCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTA
*
3680 AGAGATTGGTGTCT
65 AGAGATTGGTGTGT
* * * * * * **
3694 CTTCAAT-TTCCCTCTGATTATGATAAAAGATCGGATGTTTCAATCTGCCTCATGATCAAGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
3758 GAGATTGGTGTGT
66 GAGATTGGTGTGT
* * ** * * * * *
3771 CTTCAATCTACCCTCTGATTAGGGTAAAATATCAGATGGTTCAATATGTCCCATGATCAGGGCAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
** *
3836 GAGATTAATATGT
66 GAGATTGGTGTGT
* * * * ** *
3849 CTTCAATCTGCGCTCTGATTAGGGTAAAAGATCGAATGCTTCTATCTGTACCATGATCGGGATAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
3914 GAGATTGGTGTAT
66 GAGATTGGTGTGT
* * * * *
3927 CTTCAATCTACCCTTTGATTAGGGTAAAAGATCGGATGCTTCAATCTGCCTCATGATTGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
3992 GAGATTAGTGTGT
66 GAGATTGGTGTGT
* * * * *
4005 CTTCAATCTACCCTCTGATTAGGGTAAAAGATCGAATGCTTCTATCTGCCCCATGATTGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
4070 GAGATTGGTGTGT
66 GAGATTGGTGTGT
* * * * **
4083 CTTTAATTTGCCCTCTAATTAGGGTAAGAGATTGGATATTTCAATCTGCCCCATGATCGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
4148 GAGATTGGATGATGT
66 GAGATTGG-TG-TGT
* * * * * *
4163 -TTACAATCTGCCCTCTAATTAGGGTAAGAGATTGGACGGTTGTAATCTGTCCCATGATCGGGGT
1 CTT-CAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTT-CAATCTGCCCCATGATCGGGGT
4227 AAGAGATTGGTGTGT
64 AAGAGATTGGTGTGT
* ** *
4242 CTTCAATCTACCCTCTGATTAGGGTAAAAGATCAGATGCTTCAATCTGTCCCATGATCGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
4307 GAGATTGGAGTGT
66 GAGATTGGTGTGT
* * * *
4320 CTTCAATCTGCCCTCTAATTAGGGTAAAAGATCGGATGCTTCAATCTGCCTCATGATTGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
* **
4385 AAGATT-GAATGT
66 GAGATTGGTGTGT
* * * * *
4397 CTTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGTTGTTTCAATCTGCCTCGTGATCGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
4462 GAGATTGGATGATGT
66 GAGATTGG-TG-TGT
* * * * * * ** * * **
4477 TTTCAATTTACCCTCTAATTGGGGTAAGAGATTGGACAACTACTATCTATCCCATGATCGGGGTA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGA-TGCTTCAATCTGCCCCATGATCGGGGTA
4542 AGAGATTGGTGTGT
65 AGAGATTGGTGTGT
* * * * * * **
4556 CTTCAATATGCCTTCTAATTAGGGTAAAAGATTGGATGCTTCAATCTGCCTCATAACCAAGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
* *
4621 AAGATTGATGTGT
66 GAGATTGGTGTGT
* * * * *
4634 CTTCTATTTGCCCTCTGATTGGGGTAAGAGATTGGACGACTGT-AATCTGCCCCATGATCGGGGT
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATG-CT-TCAATCTGCCCCATGATCGGGGT
*
4698 AAGAGATTGGCGTGT
64 AAGAGATTGGTGTGT
* * * * * * * * *
4713 CTTCTATTTTCCCTTTGATT-GGGTTAAGAGATTTGACGACTGT-AATTTGCCCCATGATCAGGG
1 CTTCAATCTGCCCTCTGATTAGGG-TAAAAGATTGGATG-CT-TCAATCTGCCCCATGATCGGGG
4776 TAAGAGATTGGTGTGT
63 TAAGAGATTGGTGTGT
* ** * * *
4792 CTTCAATCTGCCTTCTGATTAGGGTAAAAGATCAGATGCTTAAATTTTCCCCATGATCGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
4857 GTGATTGGTGTGT
66 GAGATTGGTGTGT
* * * *
4870 CTTCAATCTACCCTTTGATTAGGGTAAAAGATTGGATGCTTCAATTTACCCCATGATCGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
4935 GAGATTGGTGTGT
66 GAGATTGGTGTGT
** * *
4948 CTTCAATCTATCCTTTGATTAGGGTAAAAGATCGGATGCTTCAATCTGCCCCATGATCGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
5013 GAGATTGTTGTGT
66 GAGATTGGTGTGT
* * * *
5026 CTTCAATCTACCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCAGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
5091 GAGATTGATGTGT
66 GAGATTGGTGTGT
* *
5104 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
5169 GAGATTG
66 GAGATTG
5176 AATGGTGATG
Statistics
Matches: 1405, Mismatches: 213, Indels: 51
0.84 0.13 0.03
Matches are distributed among these distances:
77 135 0.10
78 811 0.58
79 256 0.18
80 110 0.08
81 61 0.04
82 18 0.01
85 1 0.00
86 3 0.00
87 10 0.01
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (78 bp):
CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
GAGATTGGTGTGT
Done.