Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000644.1 Kokia drynarioides strain JFW-HI SEQ_111618, 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: 85848
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 43 characters in sequence are not A, C, G, or T
Found at i:44689 original size:26 final size:27
Alignment explanation
Indices: 44650--44703 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
44640 TAATTTAAAA
* *
44650 AATTTAATGAATAAATAA-AAAATTAAT
1 AATTAAATGAATAAA-AATAAAATCAAT
44677 AATTAAATG-ATAAAAATAAAATCAAT
1 AATTAAATGAATAAAAATAAAATCAAT
44703 A
1 A
44704 TTTTAGTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.08
26 14 0.58
27 8 0.33
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (27 bp):
AATTAAATGAATAAAAATAAAATCAAT
Found at i:48668 original size:132 final size:132
Alignment explanation
Indices: 48417--48681 Score: 363
Period size: 132 Copynumber: 2.0 Consensus size: 132
48407 ACACAGTTAG
* * *
48417 AAACCAAGAAAGTGAAAGGATCTCTTCCTGATAACTTCTTTGATAGGGGTGAAACCAAGTTACCT
1 AAACAAAGAAAGTGAAAGGATCTCTTCCTGATAACTTCTTTGATAAGGATGAAACCAAGTTACCT
* **
48482 ATGAATCTTATGAAGCCTCCTAGGGAGAATAAACTGGCAGCAAAGCAGGCTAGTGCTCCAGAAAC
66 ATGAATCTCATGAAGCCTCCTAGGGAGAATAAACAAGCAGCAAAGCAGGCTAGTGCTCCAGAAAC
48547 CA
131 CA
* * * **
48549 AAACAAAGCAAGTTAAAGGATCTCTTCCTGATGACTTCTTTGATAAGGATGATTCCAAGTTACCT
1 AAACAAAGAAAGTGAAAGGATCTCTTCCTGATAACTTCTTTGATAAGGATGAAACCAAGTTACCT
* * **
48614 ATGAATGC-CATGAAGCCTCCTAGGGAGAATATAGAAGCTTCAGAA-CAGGCTAGTGCTCCAGAA
66 ATGAAT-CTCATGAAGCCTCCTAGGGAGAATAAACAAGCAGCA-AAGCAGGCTAGTGCTCCAGAA
48677 ACCA
129 ACCA
48681 A
1 A
48682 GCAAGTAAAG
Statistics
Matches: 116, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
132 113 0.97
133 3 0.03
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.23
Consensus pattern (132 bp):
AAACAAAGAAAGTGAAAGGATCTCTTCCTGATAACTTCTTTGATAAGGATGAAACCAAGTTACCT
ATGAATCTCATGAAGCCTCCTAGGGAGAATAAACAAGCAGCAAAGCAGGCTAGTGCTCCAGAAAC
CA
Found at i:48734 original size:132 final size:129
Alignment explanation
Indices: 48426--48717 Score: 301
Period size: 132 Copynumber: 2.3 Consensus size: 129
48416 GAAACCAAGA
* * * ** * * ** *
48426 AAGTGAAAGGATCTCTTCCTGATAACTTCTTTGATAGGGGTGAAACCAAGTTACCTATGAATCTT
1 AAGTTAAAGGAGCTCTACCTGAGGACTTCTTTGATAAGGATGATTCCAAGTTACCTATGAATCTC
**
48491 ATGAAGCCTCCTAGGGAGAATAAACTGGCAGCAAAGCAGGCTAGTGCTCCAGAAACCAAAACAAA
66 ATGAAGCCTCCTAGGGAGAATAAACAAGCAGCAAAGCAGGCTAGTGCTCCAGAAACC---ACAAA
48556 GC
128 GC
* * *
48558 AAGTTAAAGGATCTCTTCCTGATGACTTCTTTGATAAGGATGATTCCAAGTTACCTATGAATGC-
1 AAGTTAAAGGAGCTCTACCTGAGGACTTCTTTGATAAGGATGATTCCAAGTTACCTATGAAT-CT
* * **
48622 CATGAAGCCTCCTAGGGAGAATATAGAAGCTTCAGAA-CAGGCTAGTGCTCCAGAAA-C-C-AAG
65 CATGAAGCCTCCTAGGGAGAATAAACAAGCAGCA-AAGCAGGCTAGTGCTCCAGAAACCACAAAG
48683 C
129 C
48684 AAG-TAAAGGGAGCTCTACCTGAAGGA-TTCTTTGA
1 AAGTTAAA-GGAGCTCTACCTG-AGGACTTCTTTGA
48718 CAATAAGGAA
Statistics
Matches: 140, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
125 4 0.03
126 26 0.19
127 4 0.03
131 1 0.01
132 102 0.73
133 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (129 bp):
AAGTTAAAGGAGCTCTACCTGAGGACTTCTTTGATAAGGATGATTCCAAGTTACCTATGAATCTC
ATGAAGCCTCCTAGGGAGAATAAACAAGCAGCAAAGCAGGCTAGTGCTCCAGAAACCACAAAGC
Found at i:60278 original size:4 final size:4
Alignment explanation
Indices: 60271--60301 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
60261 TATATATATA
60271 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
60302 AACTTAAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:71922 original size:21 final size:21
Alignment explanation
Indices: 71873--71930 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
71863 GACATTTATC
* *
71873 TACGATTAATG-TAAAAATAAT
1 TACGA-TAATGATAAAATTAAG
71894 TACGATAATGATAAAATTAAG
1 TACGATAATGATAAAATTAAG
* *
71915 TACTATAA-CATAAAAT
1 TACGATAATGATAAAAT
71931 AAAAAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 12 0.38
21 20 0.62
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (21 bp):
TACGATAATGATAAAATTAAG
Found at i:73774 original size:2 final size:2
Alignment explanation
Indices: 73767--73799 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
73757 ATGGGGATAG
*
73767 CT CT CT CT CA CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
73800 ATATTCATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.52, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:81265 original size:23 final size:23
Alignment explanation
Indices: 81227--81280 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
81217 GTTTTATGGC
81227 TTTTAAATATTATTTTACAAA-A
1 TTTTAAATATTATTTTACAAATA
* *
81249 TTTTAAAGTATTTTTTTATAAATA
1 TTTTAAA-TATTATTTTACAAATA
81273 TTTCTAAA
1 TTT-TAAA
81281 AAAATTCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 7 0.26
23 12 0.44
24 4 0.15
25 4 0.15
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTAAATATTATTTTACAAATA
Found at i:81607 original size:42 final size:43
Alignment explanation
Indices: 81549--81829 Score: 300
Period size: 42 Copynumber: 6.6 Consensus size: 43
81539 TTATGAGGAA
* * ** *
81549 AAACGCCACTATAGAACATGGTCTTTAGCAACGC-TTTCCCAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
*
81591 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCCTTT-CCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * *
81633 AAACGCCGCTATAGACCATGGGCTTTAGCGGCGCTTTT-CCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * * *
81675 AAACGCTGTTACAGACCATGAG-CTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGAACATG-GTCTTTAGCGGCGCTTTTCCCAC
**
81718 AAACGCCGCTAAAGAACATGGTCTTTAGCGATGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * * * * *
81761 AAACGCCGTTAGAGACCATGATCTCTAGCGGCACTTTTCCCGC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* *
81804 AAACGCCGTTAAAAAACATGGTCTTT
1 AAACGCCGCTAAAGAACATGGTCTTT
81830 GTACTTCAAA
Statistics
Matches: 202, Mismatches: 33, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
42 105 0.52
43 97 0.48
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
Found at i:81744 original size:43 final size:42
Alignment explanation
Indices: 81549--81829 Score: 278
Period size: 43 Copynumber: 6.6 Consensus size: 42
81539 TTATGAGGAA
* * ** *
81549 AAACGCCACTATAGAACATGGTCTTTAGCAACGCTTTCCCAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCAC
81591 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCCTTT-CCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCG-CTTTCCCAC
* * * *
81633 AAACGCCGCTATAGACCATGGGCTTTAGCGGCGCTTTTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCAC
* * * * *
81675 AAACGCTGTTACAGACCATGAG-CTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGAACATG-GTCTTTAGCGGCGC-TTTCCCAC
**
81718 AAACGCCGCTAAAGAACATGGTCTTTAGCGATGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGC-TTTCCCAC
* * * * * * *
81761 AAACGCCGTTAGAGACCATGATCTCTAGCGGCACTTTTCCCGC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGC-TTTCCCAC
* *
81804 AAACGCCGTTAAAAAACATGGTCTTT
1 AAACGCCGCTAAAGAACATGGTCTTT
81830 GTACTTCAAA
Statistics
Matches: 202, Mismatches: 32, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
41 4 0.02
42 96 0.48
43 102 0.50
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCAC
Found at i:81822 original size:86 final size:85
Alignment explanation
Indices: 81549--81829 Score: 332
Period size: 84 Copynumber: 3.3 Consensus size: 85
81539 TTATGAGGAA
* * * * * * *
81549 AAACGCCACTATAGAACATGGTCTTTAGCAACGC-TTTCCCAAAAACGCCGCTAAAGAACATGGT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTTCCCACAAACGCCGTTAAAGACCATGAT
*
81613 CTTTAGCGGCGCCTTTCCAC
66 CTTTAGCGGCGCTTTTCCAC
* * * * * * *
81633 AAACGCCGCTATAGACCATGGGCTTTAGCGGCGCTTTT-CCACAAACGCTGTTACAGACCATGAG
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTTCCCACAAACGCCGTTAAAGACCATGAT
81697 CTTTAGCGGCGCTTTTTCCAC
66 CTTTAGCGGCGC-TTTTCCAC
* *
81718 AAACGCCGCTAAAGAACATGGTCTTTAGCGATGCTTTTCCCACAAACGCCGTTAGAGACCATGAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTTCCCACAAACGCCGTTAAAGACCATGAT
* * *
81783 CTCTAGCGGCACTTTTCCCGC
66 CTTTAGCGGCGCTTTT-CCAC
* *
81804 AAACGCCGTTAAAAAACATGGTCTTT
1 AAACGCCGCTAAAGAACATGGTCTTT
81830 GTACTTCAAA
Statistics
Matches: 167, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
84 60 0.36
85 47 0.28
86 60 0.36
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (85 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTTCCCACAAACGCCGTTAAAGACCATGAT
CTTTAGCGGCGCTTTTCCAC
Found at i:82897 original size:41 final size:41
Alignment explanation
Indices: 82837--83289 Score: 550
Period size: 41 Copynumber: 11.0 Consensus size: 41
82827 ATTTAAATAA
* * * * *
82837 TTAGCGGCGTTTTTCCCATAAGCGTCACTATTGCTCTAACCT
1 TTAGCGGCG-CTTGCCCATAAGCGCCGCTATTGCTCTGACCT
* *
82879 TTAGCGGCGCTTTCCCATAAGCACCGCTATTGCTCTGACCT
1 TTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCT
* *
82920 TTAGCGGCGCTT-TCCATAAGCACCGCTATTGCTCTGACCT
1 TTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCT
* * * * * * *
82960 TTAGCTGCGCTTGCCTATAAGTGTCGTTATTGATCTGATCT
1 TTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCT
* * *
83001 TTAGCGACGCTTGGCCATAAGCGTCGCTATTGCTCTGACCT
1 TTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCT
* * * * *
83042 TTAGCGGTGCTTGCCCATAAACGGCGCTATTGATCTAACCT
1 TTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCT
* *
83083 TTAGCGGCGCTTGGCCATAAACGCCGCTATTGCTCTGACCT
1 TTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCT
*
83124 TTAGCGGCGCTTGCCCATAAGCGCCGCTAGTGCTCTGACCT
1 TTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCT
* * *
83165 TTAGCGGCTCTTTCCTATAAGCGCCGCTATTGCTCTGACCT
1 TTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCT
* *
83206 TTAGCGGTGCTTGCCCATAAGCACCGCTATTTGCTCTGACCT
1 TTAGCGGCGCTTGCCCATAAGCGCCGCTA-TTGCTCTGACCT
* * * *
83248 TTAGTGACGCTTGACTATAAGCGCCGCTATTGCTCT-ACCT
1 TTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCT
83288 TT
1 TT
83290 TGCAGCGTTT
Statistics
Matches: 356, Mismatches: 53, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
40 44 0.12
41 268 0.75
42 44 0.12
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.32
Consensus pattern (41 bp):
TTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCT
Done.