Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000334.1 Kokia drynarioides strain JFW-HI SEQ_111105, 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: 28150
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--29 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30 TAGTAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1604 original size:99 final size:99
Alignment explanation
Indices: 1433--1632 Score: 346
Period size: 99 Copynumber: 2.0 Consensus size: 99
1423 GTGGTTAAGC
*
1433 AGGGGAATGATCAGTCTCATAGTGAAGTGAATGATGTGCAGAGAAAGGTGGGTAAGATGGGAAAG
1 AGGGGAATGATCAGTCTCATAGTGAAGTGAAGGATGTGCAGAGAAAGGTGGGTAAGATGGGAAAG
*
1498 CGAAAGCGTGGGAGACCGCCCAAGTTGCTGGAGA
66 CGAAAGCGTGGGAGACCACCCAAGTTGCTGGAGA
* *
1532 AGGGGAATGATCAGTCTCGTAGTGAAGTGAAGGATGTGCAGAGTAAGGTGGGTAAGATGGGAAAG
1 AGGGGAATGATCAGTCTCATAGTGAAGTGAAGGATGTGCAGAGAAAGGTGGGTAAGATGGGAAAG
* *
1597 CGGAAGCGTGGGAGACCACCCAAGTTTCTGGAGA
66 CGAAAGCGTGGGAGACCACCCAAGTTGCTGGAGA
1631 AG
1 AG
1633 AATGGGTCTG
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 95 1.00
ACGTcount: A:0.32, C:0.12, G:0.39, T:0.17
Consensus pattern (99 bp):
AGGGGAATGATCAGTCTCATAGTGAAGTGAAGGATGTGCAGAGAAAGGTGGGTAAGATGGGAAAG
CGAAAGCGTGGGAGACCACCCAAGTTGCTGGAGA
Found at i:8861 original size:20 final size:20
Alignment explanation
Indices: 8836--8887 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
8826 ATGAATTTTA
8836 AACCTTAAACTTCAAACTCG
1 AACCTTAAACTTCAAACTCG
* ** *
8856 AACCTTAAATTTTGAACTTG
1 AACCTTAAACTTCAAACTCG
*
8876 AACCTCAAACTT
1 AACCTTAAACTT
8888 GAGATTCGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (20 bp):
AACCTTAAACTTCAAACTCG
Found at i:11228 original size:81 final size:79
Alignment explanation
Indices: 11089--12506 Score: 1159
Period size: 81 Copynumber: 17.5 Consensus size: 79
11079 GTCTTTTTCA
* * * * * * * *
11089 ACTCCATAACCCGGCTTATATTTGCTTTCAAGGCGTGAAACATGAGAAGA-TGAGGAAGATCTCT
1 ACTCCATAA-CCGGTTTGTATTTGCTTTCAAGGCGTGCAATACGAGATGAGGGA-GAAGA-ATCT
*
11153 TTTCCTCTGCTTCATCT
63 TTTCCTCTGCTTCATCC
* *
11170 GCTCCATAATCCGGTTTGTATTTGCTCTCAAGGCGTGCAATACGAGATGAGGGAGAAGAATTCTT
1 ACTCCATAA-CCGGTTTGTATTTGCTTTCAAGGCGTGCAATACGAGATGAGGGAGAAGAA-TCTT
11235 TTCCTCTGCTTCATCC
64 TTCCTCTGCTTCATCC
* * * * *
11251 GCTCCATAATCCGGTTTGTATTTGCTTTCAAGACGTG-ACATGA-AAGAAGA-CGAGGAAGAACT
1 ACTCCATAA-CCGGTTTGTATTTGCTTTCAAGGCGTGCA-AT-ACGAGATGAGGGA-GAAGAA-T
*
11313 CTTTTCCTCTGCTCCATCC
61 CTTTTCCTCTGCTTCATCC
* * * * *
11332 ACTACATAACCGGGTTTGTATTTGCTCTCAAGGCGTGCAATGCGAGGA-GAGGGAGAATAATTAT
1 ACTCCATAACC-GGTTTGTATTTGCTTTCAAGGCGTGCAATACGA-GATGAGGGAGAAGAA-TCT
*
11396 TTTCCTCTGCTCCATCC
63 TTTCCTCTGCTTCATCC
* * * *
11413 ACTACATAACCAGGTTTGTATTTGCTCTCAAGGTGTGCAATACGAGATGAGGTAGAAGAATTCTT
1 ACTCCATAACC-GGTTTGTATTTGCTTTCAAGGCGTGCAATACGAGATGAGGGAGAAGAA-TCTT
11478 TTCCTCTGCTTCATCC
64 TTCCTCTGCTTCATCC
* * * * * * *
11494 ACTTCATAACTCGGCTTGTATTTGTTTTCAAGACGTGACATGTAAGAAGATGAGGAAG-A-AATC
1 ACTCCATAAC-CGGTTTGTATTTGCTTTCAAGGCGTG-CA-ATACG-AGATGAGGGAGAAGAATC
*
11557 TTTTCCTCTGCTCCATCC
62 TTTTCCTCTGCTTCATCC
* * * *
11575 ACTGCATAACCGTGTTTGTATTTGCTCTCGAGGTGTGCAATACGAGATGAGGGAGAAGAACTCTT
1 ACTCCATAACCG-GTTTGTATTTGCTTTCAAGGCGTGCAATACGAGATGAGGGAGAAGAA-TCTT
11640 TTCCTCTGCTTCATCC
64 TTCCTCTGCTTCATCC
* * * * * * *
11656 ACTGCATAACTCGGCTTGTATTTGTTTTCAAGACGTGACATGTAAGAAGATGAGGAAG-A-AATC
1 ACTCCATAAC-CGGTTTGTATTTGCTTTCAAGGCGTG-CA-ATACG-AGATGAGGGAGAAGAATC
*
11719 TTTTCCTCTGCTCCATCC
62 TTTTCCTCTGCTTCATCC
* * * * * *
11737 ACTGCATAACCGGGTTTATATTTGCTCTCGAGGTGTGCAATACGAGATGAGGGAAAAGAACTCTT
1 ACTCCATAACC-GGTTTGTATTTGCTTTCAAGGCGTGCAATACGAGATGAGGGAGAAGAA-TCTT
11802 TTCCTCTGCTTCATCC
64 TTCCTCTGCTTCATCC
* * * * * *
11818 ACTGCATAACTCGGCTTGTATTTGTTTTCAAGGCGTGACATGTAAGAAGATGAGGAAG-A-AATC
1 ACTCCATAAC-CGGTTTGTATTTGCTTTCAAGGCGTG-CA-ATACG-AGATGAGGGAGAAGAATC
*
11881 TTTTCCTCTGCTCCATCC
62 TTTTCCTCTGCTTCATCC
* * * * * *
11899 ACTGCATAACCGGGTTTATATTTGCTCTCGAGGTGTGCAATACCAGATGAGGGAGAAGAATTCTT
1 ACTCCATAACC-GGTTTGTATTTGCTTTCAAGGCGTGCAATACGAGATGAGGGAGAAGAA-TCTT
11964 TTCCTCTGCTTCATCC
64 TTCCTCTGCTTCATCC
* * * * * * **
11980 ACTACATAACTCGGCTTGTATTTGTTTTCAAGACGTGACATGTA--AGAAGA-CAAGGAAGAACT
1 ACTCCATAAC-CGGTTTGTATTTGCTTTCAAGGCGTG-CA-ATACGAGATGAGGGA-GAAGAA-T
*
12042 CTTTCCCTCTG-TTCCATCC
61 CTTTTCCTCTGCTT-CATCC
** * *
12061 ACTTGATAACTGGGTTTGTATTTGCTCTCAAGGCGTGCAATACGAGATGAGGGAGAAGAACTCTT
1 ACTCCATAAC-CGGTTTGTATTTGCTTTCAAGGCGTGCAATACGAGATGAGGGAGAAGAA-TCTT
* *
12126 TTCCTCTACTTCACCC
64 TTCCTCTGCTTCATCC
* *
12142 ACTCCATAGCCGAGTTTGTATTGGCTTTCAAGGCGTGCAATACGAGATGAGGGAGAAGAATTCTT
1 ACTCCATAACCG-GTTTGTATTTGCTTTCAAGGCGTGCAATACGAGATGAGGGAGAAGAA-TCTT
* * *
12207 GTCCTTTTCTTCATCC
64 TTCCTCTGCTTCATCC
* * * *** * *
12223 ACTCCATAACCTGGCTTGTATGTGCTTTCAAGGCGTGAAATGTAAGAAGA-CGAGGAAGAACTCT
1 ACTCCATAACC-GGTTTGTATTTGCTTTCAAGGCGTGCAATACGAGATGAGGGA-GAAGAA-TCT
12287 TTTCCTCTGCTTCATCC
63 TTTCCTCTGCTTCATCC
* * * *
12304 ACTCCATACCCGAGTTTGTATTGGCTTTCAAGGCGTGGAATGTAAGAAGATGA--G-GAAGAACT
1 ACTCCATAACCG-GTTTGTATTTGCTTTCAAGGCGTGCAA--TACG-AGATGAGGGAGAAGAA-T
* *
12366 CTTTTCCTCCGCTCCATCC
61 CTTTTCCTCTGCTTCATCC
* * *** * *
12385 ACTCCATAACCAGGTTTGTATTTGCTTTCAAGGTGTGAAATGTAAGAAGA-CGAGGAAGAACTCT
1 ACTCCATAACC-GGTTTGTATTTGCTTTCAAGGCGTGCAATACGAGATGAGGGA-GAAGAA-TCT
* *
12449 TGTCCTCTTCTTCATCC
63 TTTCCTCTGCTTCATCC
** * * *
12466 A-TTAAGTAACCAGGTTTGTACTTGCTTTCGAGGCGTTCAAT
1 ACTCCA-TAACC-GGTTTGTATTTGCTTTCAAGGCGTGCAAT
12507 GTAAGACTGC
Statistics
Matches: 1097, Mismatches: 184, Indels: 112
0.79 0.13 0.08
Matches are distributed among these distances:
78 34 0.03
79 15 0.01
80 34 0.03
81 932 0.85
82 32 0.03
83 16 0.01
84 34 0.03
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (79 bp):
ACTCCATAACCGGTTTGTATTTGCTTTCAAGGCGTGCAATACGAGATGAGGGAGAAGAATCTTTT
CCTCTGCTTCATCC
Found at i:12485 original size:162 final size:159
Alignment explanation
Indices: 11089--12512 Score: 1366
Period size: 162 Copynumber: 8.8 Consensus size: 159
11079 GTCTTTTTCA
* * * * * *
11089 ACTCCATAACCCGGCTTATATTTGCTTTCAAGGCGTG-AA-ACATGAGAAGATGAGGAAGATCTC
1 ACTCCATAACCGGGTTTGTATTTGCTCTCAAGGTGTGCAATACA--AGAAGA-GAGGAAGAACTC
** * * *
11152 TTTTCCTCTGCTTCATCTGCTCCATAATCCGGTTTGTATTTGCTCTCAAGGCGTGCAA--TACG-
63 TTTTCCTCTGCTTCATCCACTTCATAA-CCGGTTTGTATTTGCTTTCAAGGCGTG-AATGTAAGA
* *
11214 AGATGAGGGAGAAGAATTCTTTTCCTCTGCTTCATCC
126 AGATGA--G-GAAGAAATCTTTTCCTCTGCTCCATCC
* * **
11251 GCTCCATAATCC-GGTTTGTATTTGCTTTCAAGACGTG-ACATGA-AAGAAGACGAGGAAGAACT
1 ACTCCATAA-CCGGGTTTGTATTTGCTCTCAAGGTGTGCA-AT-ACAAGAAGA-GAGGAAGAACT
* * * **
11313 CTTTTCCTCTGCTCCATCCACTACATAACCGGGTTTGTATTTGCTCTCAAGGCGTGCAATGCGAG
62 CTTTTCCTCTGCTTCATCCACTTCATAACC-GGTTTGTATTTGCTTTCAAGGCGTG-AATGTAAG
* * * * *
11378 GAGA-GGGAGAATAATTATTTTCCTCTGCTCCATCC
125 AAGATGAG-GAAGAAATCTTTTCCTCTGCTCCATCC
* * * * *
11413 ACTACATAACCAGGTTTGTATTTGCTCTCAAGGTGTGCAATACGAGATGAG-GTAGAAGAATTCT
1 ACTCCATAACCGGGTTTGTATTTGCTCTCAAGGTGTGCAATACAAGAAGAGAG--GAAGAACTCT
* * *
11477 TTTCCTCTGCTTCATCCACTTCATAACTCGGCTTGTATTTGTTTTCAAGACGTGACATGTAAGAA
64 TTTCCTCTGCTTCATCCACTTCATAAC-CGGTTTGTATTTGCTTTCAAGGCGTGA-ATGTAAGAA
11542 GATGAGGAAGAAATCTTTTCCTCTGCTCCATCC
127 GATGAGGAAGAAATCTTTTCCTCTGCTCCATCC
* * * * * *
11575 ACTGCATAACCGTGTTTGTATTTGCTCTCGAGGTGTGCAATACGAGATGAGGGAGAAGAACTCTT
1 ACTCCATAACCGGGTTTGTATTTGCTCTCAAGGTGTGCAATACAAGAAGAGAG-GAAGAACTCTT
* * * *
11640 TTCCTCTGCTTCATCCACTGCATAACTCGGCTTGTATTTGTTTTCAAGACGTGACATGTAAGAAG
65 TTCCTCTGCTTCATCCACTTCATAAC-CGGTTTGTATTTGCTTTCAAGGCGTGA-ATGTAAGAAG
11705 ATGAGGAAGAAATCTTTTCCTCTGCTCCATCC
128 ATGAGGAAGAAATCTTTTCCTCTGCTCCATCC
* * * * *
11737 ACTGCATAACCGGGTTTATATTTGCTCTCGAGGTGTGCAATACGAGATGAG-GGAAAAGAACTCT
1 ACTCCATAACCGGGTTTGTATTTGCTCTCAAGGTGTGCAATACAAGAAGAGAGG--AAGAACTCT
* * *
11801 TTTCCTCTGCTTCATCCACTGCATAACTCGGCTTGTATTTGTTTTCAAGGCGTGACATGTAAGAA
64 TTTCCTCTGCTTCATCCACTTCATAAC-CGGTTTGTATTTGCTTTCAAGGCGTGA-ATGTAAGAA
11866 GATGAGGAAGAAATCTTTTCCTCTGCTCCATCC
127 GATGAGGAAGAAATCTTTTCCTCTGCTCCATCC
* * * * * * *
11899 ACTGCATAACCGGGTTTATATTTGCTCTCGAGGTGTGCAATACCAGATGAGGGAGAAGAATTCTT
1 ACTCCATAACCGGGTTTGTATTTGCTCTCAAGGTGTGCAATACAAGAAGAGAG-GAAGAACTCTT
* * * *
11964 TTCCTCTGCTTCATCCACTACATAACTCGGCTTGTATTTGTTTTCAAGACGTGACATGTAAGAAG
65 TTCCTCTGCTTCATCCACTTCATAAC-CGGTTTGTATTTGCTTTCAAGGCGTGA-ATGTAAGAAG
** * * *
12029 ACAAGGAAGAACTCTTTCCCTCTGTTCCATCC
128 ATGAGGAAGAAATCTTTTCCTCTGCTCCATCC
** * * * * *
12061 ACTTGATAACTGGGTTTGTATTTGCTCTCAAGGCGTGCAATACGAGATGAGGGAGAAGAACTCTT
1 ACTCCATAACCGGGTTTGTATTTGCTCTCAAGGTGTGCAATACAAGAAGAGAG-GAAGAACTCTT
* * * * * *
12126 TTCCTCTACTTCACCCACTCCATAGCCGAGTTTGTATTGGCTTTCAAGGCGTGCAA--TACG-AG
65 TTCCTCTGCTTCATCCACTTCATAACCG-GTTTGTATTTGCTTTCAAGGCGTG-AATGTAAGAAG
* * * * *
12188 ATGAGGGAGAAGAATTCTTGTCCTTTTCTTCATCC
128 ATGA--G-GAAGAAATCTTTTCCTCTGCTCCATCC
* * * * * * **
12223 ACTCCATAACCTGGCTTGTATGTGCTTTCAAGGCGTGAAATGTAAGAAGACGAGGAAGAACTCTT
1 ACTCCATAACCGGGTTTGTATTTGCTCTCAAGGTGTGCAATACAAGAAGA-GAGGAAGAACTCTT
* * *
12288 TTCCTCTGCTTCATCCACTCCATACCCGAGTTTGTATTGGCTTTCAAGGCGTGGAATGTAAGAAG
65 TTCCTCTGCTTCATCCACTTCATAACCG-GTTTGTATTTGCTTTCAAGGCGT-GAATGTAAGAAG
* *
12353 ATGAGGAAGAACTCTTTTCCTCCGCTCCATCC
128 ATGAGGAAGAAATCTTTTCCTCTGCTCCATCC
* * * **
12385 ACTCCATAACCAGGTTTGTATTTGCTTTCAAGGTGTGAAATGTAAGAAGACGAGGAAGAACTCTT
1 ACTCCATAACCGGGTTTGTATTTGCTCTCAAGGTGTGCAATACAAGAAGA-GAGGAAGAACTCTT
* * * * * *
12450 GTCCTCTTCTTCATCCA-TTAAGTAACCAGGTTTGTACTTGCTTTCGAGGCGTTCAATGTAAGA
65 TTCCTCTGCTTCATCCACTTCA-TAACC-GGTTTGTATTTGCTTTCAAGGCG-TGAATGTAAGA
12513 CTGCGATGGA
Statistics
Matches: 1110, Mismatches: 118, Indels: 68
0.86 0.09 0.05
Matches are distributed among these distances:
159 4 0.00
160 5 0.00
161 13 0.01
162 1055 0.95
163 16 0.01
164 7 0.01
165 10 0.01
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (159 bp):
ACTCCATAACCGGGTTTGTATTTGCTCTCAAGGTGTGCAATACAAGAAGAGAGGAAGAACTCTTT
TCCTCTGCTTCATCCACTTCATAACCGGTTTGTATTTGCTTTCAAGGCGTGAATGTAAGAAGATG
AGGAAGAAATCTTTTCCTCTGCTCCATCC
Found at i:14056 original size:29 final size:29
Alignment explanation
Indices: 14009--14078 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 29
13999 ATATTAAATG
*
14009 TAATAATTAATAACTAATTTA-ATTAATTTCA
1 TAAT-ATTAA-AACTAA-TTAGATTAATTTAA
*
14040 TATATATTAAAAC-AATTAGATTATTTTAA
1 TA-ATATTAAAACTAATTAGATTAATTTAA
14069 TAATATTAAA
1 TAATATTAAA
14079 CAAATAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
28 11 0.31
29 12 0.34
30 3 0.09
31 7 0.20
32 2 0.06
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.44
Consensus pattern (29 bp):
TAATATTAAAACTAATTAGATTAATTTAA
Found at i:17753 original size:27 final size:27
Alignment explanation
Indices: 17723--17775 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
17713 AAAAATTATG
* *
17723 CAATAATATAAAAGCATATTATTTTTA
1 CAATAATATAAAAGAATACTATTTTTA
*
17750 CAATAATATAAATGAATACTATTTTT
1 CAATAATATAAAAGAATACTATTTTT
17776 TTTATTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.42
Consensus pattern (27 bp):
CAATAATATAAAAGAATACTATTTTTA
Found at i:18079 original size:18 final size:18
Alignment explanation
Indices: 18056--18092 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
18046 GTTTGAAATT
18056 ATATTTTAAATT-TATTTC
1 ATATTTT-AATTATATTTC
18074 ATATTTTAATTATATTTC
1 ATATTTTAATTATATTTC
18092 A
1 A
18093 AAACTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
ATATTTTAATTATATTTC
Found at i:18354 original size:23 final size:23
Alignment explanation
Indices: 18311--18357 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
18301 TCAGACCACA
18311 TTTTATCATTTTTAATTTTAATTT
1 TTTTATCATTTTTAA-TTTAATTT
18335 TTTTATCATTTTTCAA-TTAATTT
1 TTTTATCATTTTT-AATTTAATTT
18358 AATGGGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.32
24 13 0.59
25 2 0.09
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTATCATTTTTAATTTAATTT
Found at i:23007 original size:2 final size:2
Alignment explanation
Indices: 23000--23029 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
22990 TTATTATTTG
23000 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
23030 CAAATTTAAT
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:23796 original size:13 final size:13
Alignment explanation
Indices: 23780--23818 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
23770 TTTATATTTT
*
23780 TTAATATTATTAA
1 TTAATATAATTAA
* *
23793 TTAATCTAAATAA
1 TTAATATAATTAA
23806 TTAATATAATTAA
1 TTAATATAATTAA
23819 ATTTTTATTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATATAATTAA
Done.