Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006750.1 Kokia drynarioides strain JFW-HI SEQ_121348, 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: 122512
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Warning! 121 characters in sequence are not A, C, G, or T
Found at i:16835 original size:60 final size:59
Alignment explanation
Indices: 16720--16835 Score: 128
Period size: 60 Copynumber: 1.9 Consensus size: 59
16710 GTCGCTTAAC
* * *
16720 TATGAAAAGTTATAAAATAGTCATCCAACTATTAGTAAATTTATTTTTTGGTCACCCAAG
1 TATGAAAAGTTATAAAATAGTCACCCAACTATTA-CAAATTTATTTTTTGATCACCCAAG
* * *
16780 TATGAAAAGTTATAGAAT-GATCACCCAACTATT-CAATTTTGTCTTTTATGATCACC
1 TATGAAAAGTTATAAAATAG-TCACCCAACTATTACAAATTTAT-TTTT-TGATCACC
16836 AATTGGCTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
58 6 0.13
59 5 0.11
60 36 0.77
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (59 bp):
TATGAAAAGTTATAAAATAGTCACCCAACTATTACAAATTTATTTTTTGATCACCCAAG
Found at i:17671 original size:24 final size:24
Alignment explanation
Indices: 17644--17699 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
17634 AATTCTTTTC
17644 TTTTCATGTAATTAAAATAA-TTAGT
1 TTTTCAT-TAATTAAAATAATTTA-T
* *
17669 TTTTAATTAATTAAAGTAATTTA-
1 TTTTCATTAATTAAAATAATTTAT
17692 TTTTCATT
1 TTTTCATT
17700 TAGTCGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 7 0.26
24 11 0.41
25 9 0.33
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.54
Consensus pattern (24 bp):
TTTTCATTAATTAAAATAATTTAT
Found at i:19921 original size:31 final size:31
Alignment explanation
Indices: 19853--19924 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
19843 AAAAAAAATC
* * *
19853 ATTAAACCTTTCAAAATTTTTGAAAAGTCTA
1 ATTAAACCCTACAAAAGTTTTGAAAAGTCTA
* * * *
19884 AGTAAACCCTACAAAAGTTTTGAAGATTTTA
1 ATTAAACCCTACAAAAGTTTTGAAAAGTCTA
19915 ATTAAACCCT
1 ATTAAACCCT
19925 CCGAATTTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (31 bp):
ATTAAACCCTACAAAAGTTTTGAAAAGTCTA
Found at i:24980 original size:3 final size:3
Alignment explanation
Indices: 24972--24998 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
24962 TTAATCCTTC
24972 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
24999 CCAAAAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:32212 original size:23 final size:22
Alignment explanation
Indices: 32173--32221 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
32163 AAATTAATTG
32173 AAATTTAATATAATACATATTAT
1 AAATTTAATATAATACAT-TTAT
* *
32196 AAATTTCAA-ATACTACATTTTT
1 AAATTT-AATATAATACATTTAT
32218 AAAT
1 AAAT
32222 ATTTTACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 14 0.61
24 2 0.09
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATTTAATATAATACATTTAT
Found at i:44055 original size:5 final size:5
Alignment explanation
Indices: 44041--44075 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
44031 TAAATTATTT
*
44041 AAAG- AAAGA AAAGA AGAGA AAAGA AAAGA AAAGA A
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA A
44076 TTAATGGCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:56821 original size:21 final size:21
Alignment explanation
Indices: 56782--56821 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
56772 ATATCAGATT
* * *
56782 CATTATAAAAACATTCATAAA
1 CATTAAAAAAAAATGCATAAA
56803 CATTAAAAAAAAATGCATA
1 CATTAAAAAAAAATGCATA
56822 TATACATCTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.60, C:0.12, G:0.03, T:0.25
Consensus pattern (21 bp):
CATTAAAAAAAAATGCATAAA
Found at i:60254 original size:30 final size:30
Alignment explanation
Indices: 60209--60285 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 30
60199 TTTTTAATCC
* *
60209 AATTTTATACATGAACTCGACTCTTTTCCT
1 AATTTGATACCTGAACTCGACTCTTTTCCT
* *
60239 AATTTGATACCTGAACTTGACTCTTTTCTT
1 AATTTGATACCTGAACTCGACTCTTTTCCT
*
60269 AATTTGATACCTAAACT
1 AATTTGATACCTGAACT
60286 TGTCAAGCGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.43
Consensus pattern (30 bp):
AATTTGATACCTGAACTCGACTCTTTTCCT
Found at i:65292 original size:28 final size:29
Alignment explanation
Indices: 65259--65313 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
65249 GGCTTCTATA
*
65259 TTCAATTTGGTATC-TGAGTTT-ATTTTGT
1 TTCAATTCGGTA-CATGAGTTTGATTTTGT
65287 TTCAATTCGGTACATGAGTTTGATTTT
1 TTCAATTCGGTACATGAGTTTGATTTT
65314 AATGTTCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 1 0.04
28 18 0.75
29 5 0.21
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (29 bp):
TTCAATTCGGTACATGAGTTTGATTTTGT
Found at i:73553 original size:42 final size:42
Alignment explanation
Indices: 73470--73556 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
73460 AATACAATTG
* * *
73470 TAGCATAATTCCATCAAAATTTATGCTCCAAAACTATCCAAA
1 TAGCATAATGCAATCAAAATTTATGCTCCAAAACTACCCAAA
*
73512 TAGCATAATGCAATCAAAATTTATGCTCTAAAA-TCACCCAAA
1 TAGCATAATGCAATCAAAATTTATGCTCCAAAACT-ACCCAAA
73554 TAG
1 TAG
73557 GGAAAACATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.03
42 39 0.98
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.28
Consensus pattern (42 bp):
TAGCATAATGCAATCAAAATTTATGCTCCAAAACTACCCAAA
Found at i:77791 original size:7 final size:7
Alignment explanation
Indices: 77779--77806 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
77769 AATTGTACAT
77779 CATGTCA
1 CATGTCA
77786 CATGTCA
1 CATGTCA
77793 CATGTCA
1 CATGTCA
77800 CATGTCA
1 CATGTCA
77807 AATAAACTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (7 bp):
CATGTCA
Found at i:78067 original size:17 final size:17
Alignment explanation
Indices: 78045--78094 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
78035 TTACACCATT
*
78045 ATTCAACTCTTACTCTA
1 ATTCAACTCTAACTCTA
*
78062 ATTCAACAT-TAACTTTA
1 ATTCAAC-TCTAACTCTA
78079 ATTCAACTCTGAACTC
1 ATTCAACTCT-AACTC
78095 AACGAGTGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 1 0.04
17 21 0.78
18 5 0.19
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (17 bp):
ATTCAACTCTAACTCTA
Found at i:78595 original size:14 final size:14
Alignment explanation
Indices: 78576--78611 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
78566 TAATTCAGTT
78576 TATAAATTATAAAA
1 TATAAATTATAAAA
* *
78590 TATAAATAATAGAA
1 TATAAATTATAAAA
78604 TATAAATT
1 TATAAATT
78612 GTTCAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
TATAAATTATAAAA
Found at i:81855 original size:19 final size:21
Alignment explanation
Indices: 81814--81857 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
81804 ACATATTATG
*
81814 TATAAATAATATAAATTACAA
1 TATAAATAATATAAATAACAA
*
81835 TATAAAT-A-ATAAATAATAA
1 TATAAATAATATAAATAACAA
81854 TATA
1 TATA
81858 TATTATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
20 1 0.05
21 7 0.33
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
TATAAATAATATAAATAACAA
Found at i:83661 original size:20 final size:20
Alignment explanation
Indices: 83625--83667 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
83615 TCATGCTAAC
83625 AAATAATTTAAAAATTATAA
1 AAATAATTTAAAAATTATAA
83645 AAAT-ATTTAAAAGATTATAA
1 AAATAATTTAAAA-ATTATAA
83665 AAA
1 AAA
83668 AAAAAGATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAATAATTTAAAAATTATAA
Found at i:85384 original size:24 final size:25
Alignment explanation
Indices: 85342--85388 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
85332 AGAGACGGTT
**
85342 AAAATAATTTATCCTTAAAATTTTA
1 AAAATAATTTATCAATAAAATTTTA
85367 AAAATAATTTAT-AATAAAATTT
1 AAAATAATTTATCAATAAAATTT
85389 ATTAATGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (25 bp):
AAAATAATTTATCAATAAAATTTTA
Found at i:86375 original size:6 final size:6
Alignment explanation
Indices: 86366--86391 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
86356 ATTATTTTTA
86366 TACTTT TACTTT TACTTT TACTTT TA
1 TACTTT TACTTT TACTTT TACTTT TA
86392 TCATTACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.65
Consensus pattern (6 bp):
TACTTT
Found at i:91973 original size:19 final size:20
Alignment explanation
Indices: 91935--91973 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
91925 TTTATAAAAA
* *
91935 TTTTAATATATTTTTTAATT
1 TTTTAATATATTATTAAATT
91955 TTTTAAT-TATTATTAAATT
1 TTTTAATATATTATTAAATT
91974 GATGATCTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTAATATATTATTAAATT
Found at i:95935 original size:20 final size:20
Alignment explanation
Indices: 95903--95940 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
95893 GTTGAACCAC
95903 ATTTTAAATATTT-TTTATA
1 ATTTTAAATATTTATTTATA
*
95922 ATTTTTAATGATTTATTTA
1 ATTTTAAAT-ATTTATTTA
95941 ATGGAATCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.50
20 4 0.25
21 4 0.25
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
ATTTTAAATATTTATTTATA
Found at i:96699 original size:27 final size:28
Alignment explanation
Indices: 96665--96728 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
96655 TTATCCCCTA
96665 CTTAAAAAATGCTTTTAACTTTCTTTTC
1 CTTAAAAAATGCTTTTAACTTTCTTTTC
96693 CTTAAAAAATGCTTTTAACTTTCTTTTC
1 CTTAAAAAATGCTTTTAACTTTCTTTTC
96721 CTTAAAAA
1 CTTAAAAA
96729 TTCTATCGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (28 bp):
CTTAAAAAATGCTTTTAACTTTCTTTTC
Found at i:110143 original size:19 final size:20
Alignment explanation
Indices: 110116--110153 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
110106 AGGTACAAAT
*
110116 TATATAAAAAAAAT-TCAAG
1 TATAAAAAAAAAATCTCAAG
*
110135 TATAAAAAACAAATCTCAA
1 TATAAAAAAAAAATCTCAA
110154 TTTTTAACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.63, C:0.11, G:0.03, T:0.24
Consensus pattern (20 bp):
TATAAAAAAAAAATCTCAAG
Done.