Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009932.1 Kokia drynarioides strain JFW-HI SEQ_124673, 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: 87030
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Warning! 82 characters in sequence are not A, C, G, or T
Found at i:14580 original size:5 final size:5
Alignment explanation
Indices: 14551--14579 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
14541 CAAATACTAG
14551 CTTTT CTTTT CTTTT CTTTT CTTTT -TTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
14580 TGGGGTGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
CTTTT
Found at i:16658 original size:17 final size:17
Alignment explanation
Indices: 16638--16671 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16628 TCAACCTGTG
*
16638 TGATGGAATAGTAGTTC
1 TGATGGAATACTAGTTC
16655 TGATGGAATACTAGTTC
1 TGATGGAATACTAGTTC
16672 AAGTATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.35
Consensus pattern (17 bp):
TGATGGAATACTAGTTC
Found at i:17631 original size:2 final size:2
Alignment explanation
Indices: 17624--17653 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17614 CAACTAAATA
17624 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
17654 TATTGGCATT
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:18634 original size:24 final size:24
Alignment explanation
Indices: 18598--18643 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
18588 TCTTAATTTT
**
18598 TTTTTAATTTTTTAAGAAATATAA
1 TTTTTAAAATTTTAAGAAATATAA
* *
18622 TTTTTAAAATTTTTATAAATAT
1 TTTTTAAAATTTTAAGAAATAT
18644 TTTAAATTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTTAAAATTTTAAGAAATATAA
Found at i:24987 original size:13 final size:13
Alignment explanation
Indices: 24969--24993 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24959 TCAAGGCAAA
24969 TAATGCTATCAAC
1 TAATGCTATCAAC
24982 TAATGCTATCAA
1 TAATGCTATCAA
24994 TACTTAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
TAATGCTATCAAC
Found at i:31090 original size:6 final size:6
Alignment explanation
Indices: 31076--31111 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
31066 AACAGAAGAG
*
31076 AGTGGA AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA
1 AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA
31112 GAGGCAACTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.36, T:0.17
Consensus pattern (6 bp):
AGTGAA
Found at i:42322 original size:21 final size:21
Alignment explanation
Indices: 42275--42324 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
42265 AAATAATTAC
42275 ATTTATTTTCTTTAAATTAAG
1 ATTTATTTTCTTTAAATTAAG
* * *
42296 AGTTATTTT-TTTAATTTCATG
1 ATTTATTTTCTTTAAATT-AAG
42317 ATTTATTT
1 ATTTATTT
42325 ATTTGTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (21 bp):
ATTTATTTTCTTTAAATTAAG
Found at i:42412 original size:26 final size:26
Alignment explanation
Indices: 42374--42425 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
42364 GTTATGTAAA
*
42374 CGACTATCCAAAAGAAGGCTTAGAAG
1 CGACTATCCAAAAGAAGACTTAGAAG
*
42400 CGACTATCTAAAAGAAGACTTAGAAG
1 CGACTATCCAAAAGAAGACTTAGAAG
42426 ACAATAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.17
Consensus pattern (26 bp):
CGACTATCCAAAAGAAGACTTAGAAG
Found at i:48191 original size:20 final size:20
Alignment explanation
Indices: 48166--48204 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
48156 TCGTTCTTTA
48166 ATTGATATATAATAAAATAG
1 ATTGATATATAATAAAATAG
*
48186 ATTGATATATAGTAAAATA
1 ATTGATATATAATAAAATA
48205 CCCAAGACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (20 bp):
ATTGATATATAATAAAATAG
Found at i:52670 original size:133 final size:133
Alignment explanation
Indices: 52431--52699 Score: 484
Period size: 133 Copynumber: 2.0 Consensus size: 133
52421 ATTGGAGGGT
* *
52431 GGGATAGTATGTCTGACCTATGTTCCATTAGATTTTCAATTAGCAAATGTCCTAACAAAGGGGTT
1 GGGATAGTATGTATGACCTATGTTCCATTAGAATTTCAATTAGCAAATGTCCTAACAAAGGGGTT
*
52496 GAATAGTTTGAGTTTCTATGACCTATATCCAAGCTCAAAATGGAAGGCATCAATTCCTCGGCTTG
66 GAATAGTTTGAGTTTCTATGACCTACATCCAAGCTCAAAATGGAAGGCATCAATTCCTCGGCTTG
52561 AGG
131 AGG
52564 GGGATAGTATGTATGACCTATGTTCCATTAGAATTTCAATTAGCAAATGTCCTAACAAAGGGGTT
1 GGGATAGTATGTATGACCTATGTTCCATTAGAATTTCAATTAGCAAATGTCCTAACAAAGGGGTT
* *
52629 GAATAGTTTGAGTTTCTATGACCTACATCCAAGCTCGAAATGGAAGGCATCAATTCCTTGGCTTG
66 GAATAGTTTGAGTTTCTATGACCTACATCCAAGCTCAAAATGGAAGGCATCAATTCCTCGGCTTG
*
52694 GGG
131 AGG
52697 GGG
1 GGG
52700 GGAGGGGGGG
Statistics
Matches: 130, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
133 130 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (133 bp):
GGGATAGTATGTATGACCTATGTTCCATTAGAATTTCAATTAGCAAATGTCCTAACAAAGGGGTT
GAATAGTTTGAGTTTCTATGACCTACATCCAAGCTCAAAATGGAAGGCATCAATTCCTCGGCTTG
AGG
Found at i:62261 original size:23 final size:23
Alignment explanation
Indices: 62234--62299 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
62224 AACTATTTAA
*
62234 TTAATAAAATAATCTAGAATAAT
1 TTAATAAAATAATCTAAAATAAT
62257 TTAATATTAAATAA--TAAAATAAT
1 TTAATA--AAATAATCTAAAATAAT
*
62280 TT--TAAAATAATC-AAACTAAT
1 TTAATAAAATAATCTAAAATAAT
62300 CATCTTTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
19 6 0.16
20 7 0.19
21 2 0.05
23 16 0.43
25 6 0.16
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (23 bp):
TTAATAAAATAATCTAAAATAAT
Found at i:68877 original size:46 final size:46
Alignment explanation
Indices: 68717--68893 Score: 167
Period size: 46 Copynumber: 3.8 Consensus size: 46
68707 TAATTTTCCA
** * * * *
68717 TATTCTCCAGTTTGCAACATATGCAGGAACTAGGCACCTAAATTCG
1 TATTCTCCAGTCCGCAACATATACAGGAGCTGGGAACCTAAATTCG
* * * * * * *
68763 TATTCTCTAGTTCACAACGTATGCAGGAGCTGGAAACCTACATTCG
1 TATTCTCCAGTCCGCAACATATACAGGAGCTGGGAACCTAAATTCG
* *
68809 TACTCTCCAGTCCGTAACATATACAGGAGCTGGGAACCTAAA-TCTG
1 TATTCTCCAGTCCGCAACATATACAGGAGCTGGGAACCTAAATTC-G
* * * *
68855 TATTCTCCAGTCCGTAACATATATAGGCGTTGGGAACCT
1 TATTCTCCAGTCCGCAACATATACAGGAGCTGGGAACCT
68894 GAGCAATAAT
Statistics
Matches: 108, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
45 2 0.02
46 106 0.98
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (46 bp):
TATTCTCCAGTCCGCAACATATACAGGAGCTGGGAACCTAAATTCG
Found at i:71628 original size:18 final size:17
Alignment explanation
Indices: 71598--71632 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
71588 AAGAGAATGG
*
71598 AAAAAAAATTTAAAAAA
1 AAAAAAAAGTTAAAAAA
71615 AAAAAGAAAGTTAAAAAA
1 AAAAA-AAAGTTAAAAAA
71633 CATAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAAAAAAGTTAAAAAA
Found at i:71782 original size:44 final size:44
Alignment explanation
Indices: 71719--71807 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
71709 TAAAATGATT
71719 ATTTAACGTGCCATGTCAATTTATCTTTACATAGTTAACGGCTC
1 ATTTAACGTGCCATGTCAATTTATCTTTACATAGTTAACGGCTC
71763 ATTTAACGTGCCATGTCAATTTATCTTTACATAGTTAACGGCTC
1 ATTTAACGTGCCATGTCAATTTATCTTTACATAGTTAACGGCTC
71807 A
1 A
71808 ATGACTAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (44 bp):
ATTTAACGTGCCATGTCAATTTATCTTTACATAGTTAACGGCTC
Found at i:73069 original size:18 final size:18
Alignment explanation
Indices: 72992--73074 Score: 85
Period size: 18 Copynumber: 4.6 Consensus size: 18
72982 TCTCTTACGT
**
72992 GCCAGTATGCTTTAACGA
1 GCCAGTATGCTCAAACGA
* *
73010 GCTAGAATGCTCAAACGA
1 GCCAGTATGCTCAAACGA
* *
73028 GTCAGTGTGCTCAAACGA
1 GCCAGTATGCTCAAACGA
* * *
73046 GTCAGTATGCTCTAACAA
1 GCCAGTATGCTCAAACGA
73064 GCCAGTATGCT
1 GCCAGTATGCT
73075 ATTCCTTTTG
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (18 bp):
GCCAGTATGCTCAAACGA
Found at i:77815 original size:29 final size:28
Alignment explanation
Indices: 77767--77851 Score: 80
Period size: 29 Copynumber: 3.0 Consensus size: 28
77757 CAAACTTAAG
* *
77767 CCCTTTAAAAGTTGATAAAAATATTTTT
1 CCCTTTAAAAGTTAAAAAAAATATTTTT
* **
77795 CGCCTTTAAAAGTTAAAAAAAAAAATTGAT
1 C-CCTTTAAAAGTT-AAAAAAAATATTTTT
* * *
77825 CCCTTAAAAACTAAAAAAAAATATTTT
1 CCCTTTAAAAGTTAAAAAAAATATTTT
77852 AGACCCCTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
28 12 0.27
29 21 0.48
30 11 0.25
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (28 bp):
CCCTTTAAAAGTTAAAAAAAATATTTTT
Found at i:78815 original size:15 final size:16
Alignment explanation
Indices: 78795--78827 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
78785 AAAAGGGAAA
78795 TTAAATTTGTT-TAAG
1 TTAAATTTGTTATAAG
*
78810 TTAAATTTTTTATAAG
1 TTAAATTTGTTATAAG
78826 TT
1 TT
78828 TTGCTTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (16 bp):
TTAAATTTGTTATAAG
Found at i:80392 original size:30 final size:30
Alignment explanation
Indices: 80356--80422 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
80346 ACCACCTAAG
*
80356 ATACCCTCTCGATCTCACCTAGGTATATAA
1 ATACCCTCTCGATCTCACCTAGGCATATAA
*
80386 ATACCCTTTCGATCTCACCTAGGCATATAA
1 ATACCCTCTCGATCTCACCTAGGCATATAA
80416 ATACCCT
1 ATACCCT
80423 ATCAGTCTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.30
Consensus pattern (30 bp):
ATACCCTCTCGATCTCACCTAGGCATATAA
Found at i:80432 original size:30 final size:30
Alignment explanation
Indices: 80356--80433 Score: 113
Period size: 30 Copynumber: 2.6 Consensus size: 30
80346 ACCACCTAAG
* *
80356 ATACCCTCTCGATCTCACCTAGGTATATAA
1 ATACCCTATCGATCTCACCTAGGCATATAA
*
80386 ATACCCTTTCGATCTCACCTAGGCATATAA
1 ATACCCTATCGATCTCACCTAGGCATATAA
80416 ATACCCTATC-AGTCTCAC
1 ATACCCTATCGA-TCTCAC
80434 TGCTTGGCAC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 1 0.02
30 43 0.98
ACGTcount: A:0.29, C:0.32, G:0.09, T:0.29
Consensus pattern (30 bp):
ATACCCTATCGATCTCACCTAGGCATATAA
Found at i:81838 original size:24 final size:24
Alignment explanation
Indices: 81811--81885 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
81801 ATTTTGACTC
* *
81811 AAACAAATAAATAGATTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
81835 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* * *
81859 AAATAATTAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
81883 AAA
1 AAA
81886 GATTATTTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.28
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:82333 original size:11 final size:11
Alignment explanation
Indices: 82317--82344 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
82307 TTTTAACGAA
82317 ACGAGAGCTCC
1 ACGAGAGCTCC
82328 ACGAGAGCTCC
1 ACGAGAGCTCC
82339 ACGAGA
1 ACGAGA
82345 CACCTTAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.29, T:0.07
Consensus pattern (11 bp):
ACGAGAGCTCC
Found at i:83884 original size:24 final size:24
Alignment explanation
Indices: 83823--83885 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
83813 TAGACTAATT
* *
83823 AGAGTTTAACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
* * *
83847 AGAGTTTAATTGAAATAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
83871 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
83886 GATTATTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Done.