Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005861.1 Kokia drynarioides strain JFW-HI SEQ_120180, 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: 38416
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1506 original size:21 final size:21
Alignment explanation
Indices: 1463--1507 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1453 AAAGAAAGTT
*
1463 GGAAGAAAGAGAAAAGGGGAG
1 GGAAGAAAGAGAAAAGGCGAG
* *
1484 GGAAGAAAGAGAGAAGGCTAG
1 GGAAGAAAGAGAAAAGGCGAG
1505 GGA
1 GGA
1508 GAAGCTGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.02, G:0.47, T:0.02
Consensus pattern (21 bp):
GGAAGAAAGAGAAAAGGCGAG
Found at i:4421 original size:15 final size:15
Alignment explanation
Indices: 4401--4430 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4391 TTTGATCCCC
4401 ATCACCTGTAAATAT
1 ATCACCTGTAAATAT
4416 ATCACCTGTAAATAT
1 ATCACCTGTAAATAT
4431 CTTTAAGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (15 bp):
ATCACCTGTAAATAT
Found at i:8022 original size:20 final size:20
Alignment explanation
Indices: 7994--8179 Score: 228
Period size: 20 Copynumber: 9.3 Consensus size: 20
7984 AAGTACGAAA
*
7994 CCCCTGTATACACTTCGGTG
1 CCCCTGTATGCACTTCGGTG
* *
8014 CCTCTGTATGCACTTCGGTT
1 CCCCTGTATGCACTTCGGTG
*
8034 CCCCTATATGCACTTCGGTG
1 CCCCTGTATGCACTTCGGTG
* * *
8054 CCCCTGTATACATTTTGGTG
1 CCCCTGTATGCACTTCGGTG
*
8074 CCCCTGTATGCACTTCGATG
1 CCCCTGTATGCACTTCGGTG
**
8094 CCCCTGTATGCACTTTTGTG
1 CCCCTGTATGCACTTCGGTG
* ** *
8114 CCCTTGTATGCGTTTCAGTG
1 CCCCTGTATGCACTTCGGTG
*
8134 CCCTTGTATGCACTTCGGTG
1 CCCCTGTATGCACTTCGGTG
*
8154 CCCCTGTATGCACTTTGGTG
1 CCCCTGTATGCACTTCGGTG
8174 CCCCTG
1 CCCCTG
8180 AAAATAAATT
Statistics
Matches: 139, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 139 1.00
ACGTcount: A:0.12, C:0.32, G:0.22, T:0.35
Consensus pattern (20 bp):
CCCCTGTATGCACTTCGGTG
Found at i:16028 original size:3 final size:3
Alignment explanation
Indices: 16020--16045 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16010 CAGAATGATA
16020 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
16046 ATGAACACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16890 original size:21 final size:21
Alignment explanation
Indices: 16864--16904 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16854 TTAAAAATAT
16864 AAAATTCAAATAAATATATAA
1 AAAATTCAAATAAATATATAA
* *
16885 AAAATTCATATATATATATA
1 AAAATTCAAATAAATATATA
16905 CTCTAGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAATTCAAATAAATATATAA
Found at i:17635 original size:5 final size:5
Alignment explanation
Indices: 17625--17652 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
17615 TATTCATAAA
17625 AACCC AACCC AACCC AACCC AACCC AAC
1 AACCC AACCC AACCC AACCC AACCC AAC
17653 GGGTAGACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.57, G:0.00, T:0.00
Consensus pattern (5 bp):
AACCC
Found at i:34064 original size:97 final size:97
Alignment explanation
Indices: 33879--34072 Score: 248
Period size: 97 Copynumber: 2.0 Consensus size: 97
33869 AACTTTGAAA
*
33879 AAGGATATTTGATTATCTCGATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTTGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
* * *
33944 GAATTAGAGACAAAGAAACATTGCCTCGATTT
66 AAACTAGAAACAAAGAAACATTGCCTCGATTT
* * * * *
33976 AAGGGTATTTGATTATTTCGATTTGAGGAAAAATTGCACTTAGTAAGTTAAGGCACAAAATTTT-
1 AAGGATATTTGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCAC-AAATTTTC
* * *
34040 AAAACTCGAAATAGAAG-AATATTGCCTCGATTT
65 AAAACTAGAAACA-AAGAAACATTGCCTCGATTT
34073 TAAAGTTTTC
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
97 73 0.88
98 10 0.12
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (97 bp):
AAGGATATTTGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
AAACTAGAAACAAAGAAACATTGCCTCGATTT
Found at i:34323 original size:28 final size:28
Alignment explanation
Indices: 34292--34353 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
34282 AAAACGAGAT
*
34292 TTTTGGAT-ACCCGAGGGCAAAATAGTAA
1 TTTTGG-TCACCCGAAGGCAAAATAGTAA
* *
34320 TTTTGGTCACTCGAAGGCAAAATGGTAA
1 TTTTGGTCACCCGAAGGCAAAATAGTAA
34348 TTTTGG
1 TTTTGG
34354 GAAAGCTCGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.31
Consensus pattern (28 bp):
TTTTGGTCACCCGAAGGCAAAATAGTAA
Found at i:34462 original size:28 final size:29
Alignment explanation
Indices: 34427--34698 Score: 183
Period size: 28 Copynumber: 9.4 Consensus size: 29
34417 AAACGAGGTC
34427 AAAATTGG-AATTTTTGGAAGTTTAGGGGT
1 AAAA-TGGTAATTTTTGGAAGTTTAGGGGT
* * *
34456 AAATTGGTAATTTTTGGAAATTT-GAGGTT
1 AAAATGGTAATTTTTGGAAGTTTAG-GGGT
*
34485 AAAAATGG-AATTTTTGGAAGTTCT-GGGAT
1 -AAAATGGTAATTTTTGGAAGTT-TAGGGGT
* * **
34514 AAAATGGTAATTTCTGAAAAAAATTA-GGGT
1 AAAATGGTAATTTTTG--GAAGTTTAGGGGT
** *
34544 CAAAAATGG-AATTTTTAAAAGTTTGGGGGT
1 --AAAATGGTAATTTTTGGAAGTTTAGGGGT
** *
34574 AAAATGGTAA-TTTTGGAAAATTAGGGTT
1 AAAATGGTAATTTTTGGAAGTTTAGGGGT
**
34602 AAAATGG-AATTTTTAAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGAAGTTTAGGGGT
**
34630 AAAATGGTAATTTTTGGAA-AATA-GGGT
1 AAAATGGTAATTTTTGGAAGTTTAGGGGT
*
34657 CAAAATGG-AA-TTTTGGAAAG-TTCGGGAGT
1 -AAAATGGTAATTTTTGG-AAGTTTAGGG-GT
34686 AAAATGGTAATTT
1 AAAATGGTAATTT
34699 CTGAAAAATC
Statistics
Matches: 189, Mismatches: 33, Indels: 41
0.72 0.13 0.16
Matches are distributed among these distances:
26 6 0.03
27 11 0.06
28 75 0.40
29 63 0.33
30 18 0.10
31 9 0.05
32 7 0.04
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.35
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAAGTTTAGGGGT
Found at i:34629 original size:56 final size:57
Alignment explanation
Indices: 34393--34707 Score: 343
Period size: 56 Copynumber: 5.5 Consensus size: 57
34383 AGACATCAGA
* * *
34393 GGGTAAAATGGTAATTTTTAGAAAA-AACGAGGTCAAAATTGGAATTTTTGGAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGAAAATTA-G-GGTCAAAA-TGGAATTTTTGAAAGTTTAG
* * * * *
34452 GGGTAAATTGGTAATTTTTGGAAATTTGAGGTTAAAAATGGAATTTTTGGAAGTTCT-G
1 GGGTAAAATGGTAATTTTTGGAAAATT-AGGGTCAAAATGGAATTTTTGAAAGTT-TAG
* * * * *
34510 GGATAAAATGGTAATTTCTGAAAAAAATTAGGGTCAAAAATGGAATTTTTAAAAGTTTGG
1 GGGTAAAATGGTAATTTTTG--GAAAATTAGGGTC-AAAATGGAATTTTTGAAAGTTTAG
* *
34570 GGGTAAAATGGTAA-TTTTGGAAAATTAGGGTTAAAATGGAATTTTTAAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGAAAATTAGGGTCAAAATGGAATTTTTGAAAGTTTAG
* *
34626 GGGTAAAATGGTAATTTTTGGAAAA-TAGGGTCAAAATGGAATTTTGGAAAG-TTCG
1 GGGTAAAATGGTAATTTTTGGAAAATTAGGGTCAAAATGGAATTTTTGAAAGTTTAG
* *
34681 GGAGTAAAATGGTAATTTCTGAAAAAT
1 GG-GTAAAATGGTAATTTTTGGAAAAT
34708 CGAAGATAAA
Statistics
Matches: 220, Mismatches: 26, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
55 5 0.02
56 81 0.37
57 21 0.10
58 35 0.16
59 38 0.17
60 39 0.18
61 1 0.00
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTTGGAAAATTAGGGTCAAAATGGAATTTTTGAAAGTTTAG
Found at i:36688 original size:17 final size:17
Alignment explanation
Indices: 36642--36737 Score: 104
Period size: 17 Copynumber: 5.5 Consensus size: 17
36632 CAATATTTAT
36642 AATAAATTTAAA-TATAA
1 AATAAATTTAAACT-TAA
*
36659 ATATAAATCTAAACTTAA
1 A-ATAAATTTAAACTTAA
* *
36677 ATTAAATTTAAATTTTAA
1 AATAAATTTAAA-CTTAA
* *
36695 AACAAATTTAAATTTAA
1 AATAAATTTAAACTTAA
*
36712 AATAAATTTAATCTTAA
1 AATAAATTTAAACTTAA
36729 AATAAATTT
1 AATAAATTT
36738 TAAAATGGAT
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
17 38 0.57
18 28 0.42
19 1 0.01
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAAATTTAAACTTAA
Found at i:36695 original size:7 final size:6
Alignment explanation
Indices: 36644--36722 Score: 65
Period size: 6 Copynumber: 13.5 Consensus size: 6
36634 ATATTTATAA
* * * *
36644 TAAATT TAAATA TAAATA TAAATC TAAACT TAAA-T TAAATT TAAATTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA-TT
* * *
36692 TAAA-A CAAATT TAAATT TAAA-A TAAATT TAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAA
36723 TCTTAAAATA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
5 12 0.20
6 41 0.69
7 6 0.10
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (6 bp):
TAAATT
Found at i:36741 original size:35 final size:34
Alignment explanation
Indices: 36636--36737 Score: 116
Period size: 35 Copynumber: 2.9 Consensus size: 34
36626 GACTTTCAAT
* * *
36636 ATTTATAATAAATTTAAATATAAATATAAATCTAA
1 ATTTAAAATAAATTTAAATTTAAA-ATAAATTTAA
* * *
36671 ACTTAAATTAAATTTAAATTTTAAAACAAATTTAA
1 ATTTAAAATAAATTTAAA-TTTAAAATAAATTTAA
36706 ATTTAAAATAAATTT-AATCTTAAAATAAATTT
1 ATTTAAAATAAATTTAAAT-TTAAAATAAATTT
36738 TAAAATGGAT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
33 1 0.02
34 14 0.25
35 36 0.64
36 5 0.09
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (34 bp):
ATTTAAAATAAATTTAAATTTAAAATAAATTTAA
Done.