Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008159.1 Kokia drynarioides strain JFW-HI SEQ_122818, 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: 34537
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 76 characters in sequence are not A, C, G, or T
Found at i:1445 original size:151 final size:151
Alignment explanation
Indices: 1248--1701 Score: 671
Period size: 151 Copynumber: 3.0 Consensus size: 151
1238 GGATGTGGAA
* *
1248 TATGTGTAATTTTTCAAAATACATGAAAATTTTCAATAGGGTTTAGGTCATTTTTGAATTTGTCT
1 TATGTGTAATTTTTTAAAATACATGAAAATTTCCAATAGGGTTTAGGTCATTTTTGAATTTGTCT
* * *
1313 TATTTTTACCGGTGTTGAAAAAGTGTGTTGGGTGTTTCACAATGTTATTGAAA-CTAGATCGAAC
66 TATTTTTATCGGTGTAGAAAAAGTGTGTTGGGTGTTTCACAATGTTATTGAAATC-AGACCGAAC
*
1377 CGATCGATATATTGATTCGGAG
130 CGATCGATATATTGATTCAGAG
* *
1399 TATGTGTAATTTTTTAAAATACATGAAAATTTCCAATAGGGTTTAGGTCATTTTCGAATTTGTTT
1 TATGTGTAATTTTTTAAAATACATGAAAATTTCCAATAGGGTTTAGGTCATTTTTGAATTTGTCT
* * *
1464 TATTTTCATCGGTGTAGAAAAAGTGTTTTGGATGTTTCACAATGTTATT-AAATCAGACCGAACC
66 TATTTTTATCGGTGTAGAAAAAGTGTGTTGGGTGTTTCACAATGTTATTGAAATCAGACCGAACC
*
1528 GATCGTTATATTGATTCAGAG
131 GATCGATATATTGATTCAGAG
* * * *
1549 TATGTGTAATTTTTTAAAATACACGAAAACTTCAAATAGGGTTTAGGTCATTTTTGAATTTATCT
1 TATGTGTAATTTTTTAAAATACATGAAAATTTCCAATAGGGTTTAGGTCATTTTTGAATTTGTCT
* * * *
1614 TATTTTTATCGGTGTAAAAAAAGTGTGTTGGGTGTTCCGCAATATTATTGAAATCAGACCGAACC
66 TATTTTTATCGGTGTAGAAAAAGTGTGTTGGGTGTTTCACAATGTTATTGAAATCAGACCGAACC
* *
1679 AATCGCTATATTGA-TCTAGAG
131 GATCGATATATTGATTC-AGAG
1700 TA
1 TA
1702 AGAGAACAAA
Statistics
Matches: 273, Mismatches: 27, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
150 134 0.49
151 139 0.51
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.40
Consensus pattern (151 bp):
TATGTGTAATTTTTTAAAATACATGAAAATTTCCAATAGGGTTTAGGTCATTTTTGAATTTGTCT
TATTTTTATCGGTGTAGAAAAAGTGTGTTGGGTGTTTCACAATGTTATTGAAATCAGACCGAACC
GATCGATATATTGATTCAGAG
Found at i:1608 original size:150 final size:150
Alignment explanation
Indices: 1248--1701 Score: 662
Period size: 150 Copynumber: 3.0 Consensus size: 150
1238 GGATGTGGAA
*
1248 TATGTGTAATTTTTCAAAATACATGAAAATTTTCAATAGGGTTTAGGTCATTTTTGAATTTGTCT
1 TATGTGTAATTTTTTAAAATACATGAAAA-TTTCAATAGGGTTTAGGTCATTTTTGAATTTGTCT
* * *
1313 TATTTTTACCGGTGTTGAAAAAGTGTGTTGGGTGTTTCACAATGTTATTGAAA-CTAGATCGAAC
65 TATTTTTATCGGTGTAGAAAAAGTGTGTTGGGTGTTTCACAATGTTATTGAAATC-AGACCGAAC
*
1377 CGATCGATATATTGATTCGGAG
129 CGATCGATATATTGATTCAGAG
* *
1399 TATGTGTAATTTTTTAAAATACATGAAAATTTCCAATAGGGTTTAGGTCATTTTCGAATTTGTTT
1 TATGTGTAATTTTTTAAAATACATGAAAATTT-CAATAGGGTTTAGGTCATTTTTGAATTTGTCT
* * *
1464 TATTTTCATCGGTGTAGAAAAAGTGTTTTGGATGTTTCACAATGTTATT-AAATCAGACCGAACC
65 TATTTTTATCGGTGTAGAAAAAGTGTGTTGGGTGTTTCACAATGTTATTGAAATCAGACCGAACC
*
1528 GATCGTTATATTGATTCAGAG
130 GATCGATATATTGATTCAGAG
* * *
1549 TATGTGTAATTTTTTAAAATACACGAAAACTTCAAATAGGGTTTAGGTCATTTTTGAATTTATCT
1 TATGTGTAATTTTTTAAAATACATGAAAATTTC-AATAGGGTTTAGGTCATTTTTGAATTTGTCT
* * * *
1614 TATTTTTATCGGTGTAAAAAAAGTGTGTTGGGTGTTCCGCAATATTATTGAAATCAGACCGAACC
65 TATTTTTATCGGTGTAGAAAAAGTGTGTTGGGTGTTTCACAATGTTATTGAAATCAGACCGAACC
* *
1679 AATCGCTATATTGA-TCTAGAG
130 GATCGATATATTGATTC-AGAG
1700 TA
1 TA
1702 AGAGAACAAA
Statistics
Matches: 273, Mismatches: 25, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
149 1 0.00
150 136 0.50
151 136 0.50
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.40
Consensus pattern (150 bp):
TATGTGTAATTTTTTAAAATACATGAAAATTTCAATAGGGTTTAGGTCATTTTTGAATTTGTCTT
ATTTTTATCGGTGTAGAAAAAGTGTGTTGGGTGTTTCACAATGTTATTGAAATCAGACCGAACCG
ATCGATATATTGATTCAGAG
Found at i:4067 original size:81 final size:81
Alignment explanation
Indices: 3961--4134 Score: 312
Period size: 81 Copynumber: 2.1 Consensus size: 81
3951 TGGGGACTGA
*
3961 GGGAATGCTTGGCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGGAAGTGGAG
1 GGGAATG-ATGGCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGGAAGTGGAG
*
4026 GAAGCGCCCCAGGCTTT
65 GAAGCGCCCCAGGCATT
*
4043 GGGAATGATGGCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGTTAGGAAGTGGAGG
1 GGGAATGATGGCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGG
4108 AAGCGCCCCAGGCATT
66 AAGCGCCCCAGGCATT
4124 GGGAATGATGG
1 GGGAATGATGG
4135 TAAGGATGGC
Statistics
Matches: 89, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
81 82 0.92
82 7 0.08
ACGTcount: A:0.22, C:0.17, G:0.41, T:0.20
Consensus pattern (81 bp):
GGGAATGATGGCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGG
AAGCGCCCCAGGCATT
Found at i:4656 original size:19 final size:20
Alignment explanation
Indices: 4614--4661 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
4604 TTGAGTTAAT
* **
4614 TTTTTATATTTTATAACTTT
1 TTTTTATATATTATAACTAA
4634 TTTTTATATATTAT-ACTAA
1 TTTTTATATATTATAACTAA
*
4653 TTTTAATAT
1 TTTTTATAT
4662 TTCTCCAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTATATATTATAACTAA
Found at i:4656 original size:20 final size:21
Alignment explanation
Indices: 4610--4656 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
4600 TGACTTGAGT
*
4610 TAATTTTTTATATTTTATAAC
1 TAATTTTTTATATATTATAAC
*
4631 T-TTTTTTTATATATTAT-AC
1 TAATTTTTTATATATTATAAC
4650 TAATTTT
1 TAATTTT
4657 AATATTTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.14
20 18 0.82
21 1 0.05
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (21 bp):
TAATTTTTTATATATTATAAC
Found at i:15075 original size:25 final size:25
Alignment explanation
Indices: 15041--15093 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
15031 GAGCGTATAG
15041 ATAGATGATAAATATGGGTCAAGAA
1 ATAGATGATAAATATGGGTCAAGAA
15066 ATAGATGATAAATATGGGTCAAGAA
1 ATAGATGATAAATATGGGTCAAGAA
15091 ATA
1 ATA
15094 TTGTTTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.04, G:0.23, T:0.25
Consensus pattern (25 bp):
ATAGATGATAAATATGGGTCAAGAA
Found at i:20694 original size:23 final size:23
Alignment explanation
Indices: 20651--20694 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
20641 TCTTTTAAAA
*
20651 TTTAAAAATTTAAGAATTATTTT
1 TTTAAAAATTTAAGAAGTATTTT
*
20674 TTTAAAATTATTAA-AAGTATT
1 TTTAAAAAT-TTAAGAAGTATT
20695 AAAAAGTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (23 bp):
TTTAAAAATTTAAGAAGTATTTT
Found at i:23094 original size:23 final size:23
Alignment explanation
Indices: 23062--23109 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
23052 GATTTGACCT
*
23062 TACTTATAATTTAAAAAGTTATA
1 TACTTATAATTTAAAAACTTATA
*
23085 TACTTTTAATTTAAAAACTTATA
1 TACTTATAATTTAAAAACTTATA
23108 TA
1 TA
23110 TAATAAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (23 bp):
TACTTATAATTTAAAAACTTATA
Found at i:23372 original size:2 final size:2
Alignment explanation
Indices: 23365--23394 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23355 AAACTTTCAA
23365 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23395 TTGGTTTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31106 original size:21 final size:22
Alignment explanation
Indices: 31063--31106 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
31053 CAAATATTAT
* *
31063 AATAAATAATTTTTTTAGCCAA
1 AATAAAGAATTTTTTTAGACAA
31085 AATAAAGAATTTTTTT-GACAA
1 AATAAAGAATTTTTTTAGACAA
31106 A
1 A
31107 TCTACTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (22 bp):
AATAAAGAATTTTTTTAGACAA
Done.