Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009923.1 Kokia drynarioides strain JFW-HI SEQ_124663, 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: 74193
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:6865 original size:44 final size:43
Alignment explanation
Indices: 6799--6882 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 43
6789 ATTTAAACTA
6799 AAAATTAATTTTATTAGCTTC-AAAATAAAAAAATAAAATAGTT
1 AAAATTAATTTTATTAGCTTCAAAAATAAAAAAA-AAAATAGTT
* * *
6842 AAAATGTAATTTTATTTGTTTCAAAAATAAAATAAAAAATA
1 AAAAT-TAATTTTATTAGCTTCAAAAATAAAAAAAAAAATA
6883 AAACAATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 5 0.14
44 20 0.56
45 11 0.31
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.36
Consensus pattern (43 bp):
AAAATTAATTTTATTAGCTTCAAAAATAAAAAAAAAAATAGTT
Found at i:9179 original size:20 final size:21
Alignment explanation
Indices: 9150--9198 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
9140 ATTAACATTG
* * *
9150 TTAAAATTATTTTATTA-AAT
1 TTAAATTTATTATAATATAAT
9170 TTAAATTTATTATAATATAAT
1 TTAAATTTATTATAATATAAT
9191 TT-AATTTA
1 TTAAATTTA
9199 ATTACATTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAAATTTATTATAATATAAT
Found at i:15137 original size:17 final size:17
Alignment explanation
Indices: 15115--15147 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
15105 ATCAATATGA
15115 GAAAATATGAAA-TTGTG
1 GAAAATA-GAAAGTTGTG
15132 GAAAATAGAAAGTTGT
1 GAAAATAGAAAGTTGT
15148 CGATTACGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.27
Consensus pattern (17 bp):
GAAAATAGAAAGTTGTG
Found at i:23783 original size:156 final size:156
Alignment explanation
Indices: 23499--23804 Score: 576
Period size: 156 Copynumber: 2.0 Consensus size: 156
23489 CACTCTTAGA
*
23499 TCAAAAAATTATGGAGGCAAATAAAACCTTTTAGGTGCATATATATATAGACATATAAACAGACA
1 TCAAAAAATTATGGAGGCAAATAAAACCTTTTAGGTACATATATATATAGACATATAAACAGACA
*
23564 GTTTGGTTTTAAAAGAAAAAACAAAGGATACATATGAGCATTAACCCAAATCTAAGATTGACAAA
66 GTTTGCTTTTAAAAGAAAAAACAAAGGATACATATGAGCATTAACCCAAATCTAAGATTGACAAA
23629 AGTGCACAAGATCTACATCTATTAAT
131 AGTGCACAAGATCTACATCTATTAAT
*
23655 TCAAAAAATTATGGAGGCAAATAAAACCTTTTAGGTACATATATATATAGACATATACACAGACA
1 TCAAAAAATTATGGAGGCAAATAAAACCTTTTAGGTACATATATATATAGACATATAAACAGACA
*
23720 GTTTGCTTTTAAAAGAAAAAACATAGGATACATATGAGCATTAACCCAAATCTAAGATTGACAAA
66 GTTTGCTTTTAAAAGAAAAAACAAAGGATACATATGAGCATTAACCCAAATCTAAGATTGACAAA
23785 AGTGCACAAGATCTACATCT
131 AGTGCACAAGATCTACATCT
23805 CCCCCCAAAA
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 146 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (156 bp):
TCAAAAAATTATGGAGGCAAATAAAACCTTTTAGGTACATATATATATAGACATATAAACAGACA
GTTTGCTTTTAAAAGAAAAAACAAAGGATACATATGAGCATTAACCCAAATCTAAGATTGACAAA
AGTGCACAAGATCTACATCTATTAAT
Found at i:32081 original size:34 final size:35
Alignment explanation
Indices: 32015--32084 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
32005 ATGAAATAAT
* *
32015 TATTTTGAATATAATTATTATTTTTATGTGTAAAA
1 TATTTCGAATATAATTATTATTTTTATATGTAAAA
*
32050 TATTTCGAATATCATTATT-TTTTTATATGTAAAA
1 TATTTCGAATATAATTATTATTTTTATATGTAAAA
32084 T
1 T
32085 TAGATGAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 15 0.47
35 17 0.53
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.54
Consensus pattern (35 bp):
TATTTCGAATATAATTATTATTTTTATATGTAAAA
Found at i:51130 original size:3 final size:3
Alignment explanation
Indices: 51122--51163 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
51112 GATAAGTTTG
51122 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
51164 TTAAAAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:51878 original size:64 final size:64
Alignment explanation
Indices: 51789--51910 Score: 194
Period size: 64 Copynumber: 1.9 Consensus size: 64
51779 GTATAATAAT
*
51789 AAATTTAACTTTTAAAATAATATGTA-TTTTTTAATATTGAATGAAAGATTATATAAAAAAAAAA
1 AAATTTAACTCTTAAAATAATATGTATTTTTTTAATATT-AATGAAA-ATTATATAAAAAAAAAA
51853 A
64 A
*
51854 AAATTTAAC-CTTAAAATAATATGTATTTTTTTAATATTAATGTAAATTATATAAAAA
1 AAATTTAACTCTTAAAATAATATGTATTTTTTTAATATTAATGAAAATTATATAAAAA
51911 TAATACTTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
63 12 0.22
64 21 0.39
65 21 0.39
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (64 bp):
AAATTTAACTCTTAAAATAATATGTATTTTTTTAATATTAATGAAAATTATATAAAAAAAAAAA
Found at i:58098 original size:77 final size:77
Alignment explanation
Indices: 58006--58160 Score: 283
Period size: 77 Copynumber: 2.0 Consensus size: 77
57996 TTAATTGGAG
* * *
58006 ATTCATGCTGTGCTTTTGGCATGATAATGTTTCAATATCCAAATGAGGCCAACTATAGTTTATGA
1 ATTCATGCCGAGCTTTTGGCATGATAATGTTTCAACATCCAAATGAGGCCAACTATAGTTTATGA
58071 CTATATAATTTC
66 CTATATAATTTC
58083 ATTCATGCCGAGCTTTTGGCATGATAATGTTTCAACATCCAAATGAGGCCAACTATAGTTTATGA
1 ATTCATGCCGAGCTTTTGGCATGATAATGTTTCAACATCCAAATGAGGCCAACTATAGTTTATGA
58148 CTATATAATTTC
66 CTATATAATTTC
58160 A
1 A
58161 GCTTGGTATC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (77 bp):
ATTCATGCCGAGCTTTTGGCATGATAATGTTTCAACATCCAAATGAGGCCAACTATAGTTTATGA
CTATATAATTTC
Found at i:70799 original size:49 final size:49
Alignment explanation
Indices: 70727--70822 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 49
70717 TCAAATCTAA
*
70727 ATGATTAATACATATGGAGAGTGAGA-GATTGAGAGATTAAATGAAGACT
1 ATGATTAATACATACGGAGAGTGAGATGA-TGAGAGATTAAATGAAGACT
* * *
70776 ATGATTAATATATGCGGAGAGTGAGATGATGAGAGATTAGATGAAGA
1 ATGATTAATACATACGGAGAGTGAGATGATGAGAGATTAAATGAAGA
70823 TTAGAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 40 0.95
50 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.29, T:0.26
Consensus pattern (49 bp):
ATGATTAATACATACGGAGAGTGAGATGATGAGAGATTAAATGAAGACT
Found at i:72966 original size:96 final size:96
Alignment explanation
Indices: 72792--72973 Score: 224
Period size: 96 Copynumber: 1.9 Consensus size: 96
72782 AAGGATGCTT
* ** *
72792 GATTATCTCGATTTGAGGAAAGGTTACACCTAGTAAGTTAAGGCGCAAATTTTTAGAATCAAAAA
1 GATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTGAGAATCAAAAA
**
72857 TAAGGAAACATTGCCTCGATTAAGGGTATTC
66 TAAAAAAACATTGCCTCGATTAAGGGTATTC
* * * *
72888 GATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAGGGCGCAAATTTTCGA-AACTC-GA
1 GATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTT-GAGAA-TCAAA
* *
72951 AATAAAAAAATATTGCCTTGATT
64 AATAAAAAAACATTGCCTCGATT
72974 TTAAAGTCTT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
96 69 0.96
97 3 0.04
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTGAGAATCAAAAA
TAAAAAAACATTGCCTCGATTAAGGGTATTC
Found at i:73305 original size:29 final size:29
Alignment explanation
Indices: 73279--73442 Score: 160
Period size: 29 Copynumber: 5.6 Consensus size: 29
73269 GGGTAAAAGC
73279 GGAATTTTTGGAAGTTTC-GGGTCAAAAAT
1 GGAATTTTTGGAAGTTTCGGGGTC-AAAAT
* * *
73308 GGGATGTTGGGAAGTTT-GAGGGT-AAAAT
1 GGAATTTTTGGAAGTTTCG-GGGTCAAAAT
*
73336 GAAATTTTTTGGAAGTTTCGGGGTCAAAAT
1 GGAA-TTTTTGGAAGTTTCGGGGTCAAAAT
*
73366 AGAA-TTTTGAGAAGTTTCGGGGTCAAAAAT
1 GGAATTTTTG-GAAGTTTCGGGGTC-AAAAT
*
73396 AGG-ATTTTTGGAAG-TTCGGGGGTGAAAAT
1 -GGAATTTTTGGAAGTTTC-GGGGTCAAAAT
73425 GGAATTTTTGGATAGTTT
1 GGAATTTTTGGA-AGTTT
73443 AGGGACCTTT
Statistics
Matches: 111, Mismatches: 11, Indels: 24
0.76 0.08 0.16
Matches are distributed among these distances:
28 14 0.13
29 60 0.54
30 29 0.26
31 8 0.07
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (29 bp):
GGAATTTTTGGAAGTTTCGGGGTCAAAAT
Done.