Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013235.1 Kokia drynarioides strain JFW-HI SEQ_128254, 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: 41886
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 143 characters in sequence are not A, C, G, or T
Found at i:1450 original size:58 final size:60
Alignment explanation
Indices: 1018--1615 Score: 398
Period size: 60 Copynumber: 10.1 Consensus size: 60
1008 AGAATGAGGG
* * * * *
1018 AACACAAAAAAAAATT-AATTTTTTA-CT-AAATAAAAAGAGGGTGTCGGTCATAGCATGACT
1 AACAC-AAAAAAATTTGAATTTTTTATCTGATA-AAAAAG-GGGTGTCGGCCATTGCATGACC
* * * * * * * * * * **
1078 AATATAAAAAAAATTAAATTTTTTATTTGACT-AAAAGGGGGGGTTGACCATGGCATGGTC
1 AACACAAAAAAATTTGAATTTTTTATCTGA-TAAAAAAGGGGTGTCGGCCATTGCATGACC
* *
1138 AACACAAAAAAATTTGAAATTTTTTTATTTG--AAAAAGGGGGTGTCGGCCATTGCATGACC
1 AACACAAAAAAATTTG-AA-TTTTTTATCTGATAAAAAAGGGGTGTCGGCCATTGCATGACC
* * *
1198 AACACAAAAAAAATTTGATTTTTTTTTATCTG--AAAAAAGGGGATGTCGACCATTGCATGATC
1 AACAC-AAAAAAATTTGA--ATTTTTTATCTGATAAAAAAGGGG-TGTCGGCCATTGCATGACC
* * * * *
1260 AACACCAAAAAAATTTGAAATTTTTTTTATCT-A-AGAAAAAGGGATGTCGACTATTGCTTGGCC
1 AACA-CAAAAAAATTTG-AA--TTTTTTATCTGATA-AAAAAGGGGTGTCGGCCATTGCATGACC
* * * * * * * *
1323 AACACCAAAAAATTTGATTTTTTTTATCAGAT-AAATAGGAGTGTTGGTCATTGCATGGCC
1 AACACAAAAAAATTTGA-ATTTTTTATCTGATAAAAAAGGGGTGTCGGCCATTGCATGACC
* * *
1383 AACACCAAAAAA-TTGAATTTTTTATCTGATAAAAAAGGGGTGTCGGCCATTACATAACC
1 AACACAAAAAAATTTGAATTTTTTATCTGATAAAAAAGGGGTGTCGGCCATTGCATGACC
* * * * **
1442 AACACAAAAAAATTTG-ATTTTTTTTCAGATAAATAA-GGGTGTCAGCCATTATATGACC
1 AACACAAAAAAATTTGAATTTTTTATCTGATAAAAAAGGGGTGTCGGCCATTGCATGACC
* * * * *
1500 AACACAAAAAAATAT--ATTTTTTATCTGACAAAAAAAGGTTGTCGACCA-TGCA--A-C
1 AACACAAAAAAATTTGAATTTTTTATCTGATAAAAAAGGGGTGTCGGCCATTGCATGACC
* * * *
1554 -AC-C-CAAAAATTT-AATTTTTTTATCAGATTAAAAAGGGGTGTCGGCCATTGCATGGCC
1 AACACAAAAAAATTTGAA-TTTTTTATCTGATAAAAAAGGGGTGTCGGCCATTGCATGACC
1611 AACAC
1 AACAC
1616 TCAAAATTTT
Statistics
Matches: 427, Mismatches: 80, Indels: 63
0.75 0.14 0.11
Matches are distributed among these distances:
51 7 0.02
52 2 0.00
53 28 0.07
54 5 0.01
55 1 0.00
57 19 0.04
58 56 0.13
59 64 0.15
60 110 0.26
61 40 0.09
62 55 0.13
63 32 0.07
64 8 0.02
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (60 bp):
AACACAAAAAAATTTGAATTTTTTATCTGATAAAAAAGGGGTGTCGGCCATTGCATGACC
Found at i:2257 original size:27 final size:27
Alignment explanation
Indices: 2197--2260 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 27
2187 GGTTTTATAT
*
2197 TCCTTAAAAATTAGAAAAAAATTTAAA
1 TCCTTAAAAATTAGAAAAAAAATTAAA
*
2224 TCTCTTAAAAATT-GATAAAAAAATTAGA
1 TC-CTTAAAAATTAGA-AAAAAAATTAAA
2252 TCCTTAAAA
1 TCCTTAAAA
2261 GCTAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 11 0.33
28 22 0.67
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.31
Consensus pattern (27 bp):
TCCTTAAAAATTAGAAAAAAAATTAAA
Found at i:2996 original size:27 final size:27
Alignment explanation
Indices: 2936--2999 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 27
2926 GGTTTTATAT
*
2936 TCCTTAAAAATTAGAAAAAAATTTAAA
1 TCCTTAAAAATTAGAAAAAAAATTAAA
*
2963 TCTCTTAAAAATT-GATAAAAAAATTAGA
1 TC-CTTAAAAATTAGA-AAAAAAATTAAA
2991 TCCTTAAAA
1 TCCTTAAAA
3000 GCTAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 11 0.33
28 22 0.67
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.31
Consensus pattern (27 bp):
TCCTTAAAAATTAGAAAAAAAATTAAA
Found at i:10978 original size:31 final size:31
Alignment explanation
Indices: 10943--11014 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
10933 TAGTGTTTTT
10943 ATTTTTAATTT-AGTCACTAACGTTTTAGATC
1 ATTTTT-ATTTGAGTCACTAACGTTTTAGATC
* * *
10974 ATTTTTATTTGGGTCACTCATGTTTTAGATC
1 ATTTTTATTTGAGTCACTAACGTTTTAGATC
* *
11005 GTTTCTATTT
1 ATTTTTATTT
11015 TGACCACTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.53
Consensus pattern (31 bp):
ATTTTTATTTGAGTCACTAACGTTTTAGATC
Found at i:11023 original size:31 final size:31
Alignment explanation
Indices: 10964--11024 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
10954 AGTCACTAAC
* **
10964 GTTTTAGATCATTTTTATTTGGGTCACTCAT
1 GTTTTAGATCATTTCTATTTGGACCACTCAT
* *
10995 GTTTTAGATCGTTTCTATTTTGACCACTCA
1 GTTTTAGATCATTTCTATTTGGACCACTCA
11025 CCGTTGAATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.15, T:0.49
Consensus pattern (31 bp):
GTTTTAGATCATTTCTATTTGGACCACTCAT
Found at i:11538 original size:17 final size:17
Alignment explanation
Indices: 11489--11543 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 17
11479 CGGGAGTAAC
*
11489 AACTCTTGTTTAA-AAT
1 AACTATTGTTTAAGAAT
* * *
11505 AATTGTTG-TTGAGAAT
1 AACTATTGTTTAAGAAT
11521 AACTATTGTTTAAGAAT
1 AACTATTGTTTAAGAAT
*
11538 AGCTAT
1 AACTAT
11544 GTTCATAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 3 0.10
16 15 0.50
17 12 0.40
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (17 bp):
AACTATTGTTTAAGAAT
Found at i:16791 original size:3 final size:3
Alignment explanation
Indices: 16785--16831 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
16775 AGATGAGTTT
* * *
16785 GAA GAA GAT GAA GAT GAT GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
16832 TGTTGAGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.60, C:0.00, G:0.34, T:0.06
Consensus pattern (3 bp):
GAA
Found at i:24996 original size:24 final size:22
Alignment explanation
Indices: 24936--24997 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
24926 AAATATCCCT
24936 GAAATAAT-CAAAATTTAACAG
1 GAAATAATACAAAATTTAACAG
* *
24957 GAAAAAGATAATAAAATTTAACTAG
1 GAAATA-AT-ACAAAATTTAAC-AG
24982 GAGAATAATACAAAAT
1 GA-AATAATACAAAAT
24998 ACATTCCACG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
21 5 0.16
22 2 0.06
24 16 0.50
25 6 0.19
26 3 0.09
ACGTcount: A:0.60, C:0.06, G:0.11, T:0.23
Consensus pattern (22 bp):
GAAATAATACAAAATTTAACAG
Found at i:35731 original size:14 final size:14
Alignment explanation
Indices: 35712--35749 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
35702 TAGTGATTTA
35712 TTGTTATTATTTTG
1 TTGTTATTATTTTG
35726 TTGTTATTATTTTG
1 TTGTTATTATTTTG
35740 TTGTTATTAT
1 TTGTTATTAT
35750 ATAACTCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.13, T:0.71
Consensus pattern (14 bp):
TTGTTATTATTTTG
Found at i:38982 original size:81 final size:81
Alignment explanation
Indices: 38872--39020 Score: 192
Period size: 81 Copynumber: 1.8 Consensus size: 81
38862 AGTAAAAATA
* * * * * * *
38872 TAATTTTATTTTAATACTTTAATACTTTATAACTTTTGAAATAT-TAAATCATTTTTTTATTAAT
1 TAATTTTATTTTAATAATTTAAAACTTTATAAATTATAAAAAATCTAAATAATTTTTTTATTAAT
38936 TTAAAGAGTTAAATTG
66 TTAAAGAGTTAAATTG
* * *
38952 TAATTTTATTATTAATAATTTAAAATTTTATAAATTATAAAAAATCTAAATAATTTTTTTTTTAT
1 TAATTTTATT-TTAATAATTTAAAACTTTATAAATTATAAAAAATCTAAATAATTTTTTTATTAA
39017 TTTA
65 TTTA
39021 TATTTTAAGA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
80 10 0.18
81 27 0.47
82 20 0.35
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (81 bp):
TAATTTTATTTTAATAATTTAAAACTTTATAAATTATAAAAAATCTAAATAATTTTTTTATTAAT
TTAAAGAGTTAAATTG
Found at i:39277 original size:26 final size:27
Alignment explanation
Indices: 39246--39297 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
39236 GATCATTTTA
39246 ATTAAGTAAAAA-TAT-TTAAAATTAAC
1 ATTAAGTAAAAATTATATT-AAATTAAC
39272 ATTAAGTAAAAATTATATTAAATTAA
1 ATTAAGTAAAAATTATATTAAATTAA
39298 AAATAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 12 0.50
27 10 0.42
28 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (27 bp):
ATTAAGTAAAAATTATATTAAATTAAC
Done.