Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012888.1 Kokia drynarioides strain JFW-HI SEQ_127902, 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: 10893
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:1968 original size:8 final size:8
Alignment explanation
Indices: 1953--2012 Score: 68
Period size: 9 Copynumber: 7.0 Consensus size: 8
1943 AATTTCACCA
1953 AAAAAAAG
1 AAAAAAAG
1961 AGAAAAAGAG
1 A-AAAAA-AG
1971 AAAAAAAG
1 AAAAAAAG
1979 AAAAAAAG
1 AAAAAAAG
1987 -AAAAAAG
1 AAAAAAAG
1994 AAATAGAAAG
1 AAA-A-AAAG
2004 AAGAAAAAG
1 AA-AAAAAG
2013 GAGACGTCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
7 7 0.15
8 13 0.28
9 15 0.33
10 10 0.22
11 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1974 original size:7 final size:8
Alignment explanation
Indices: 1955--1996 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
1945 TTTCACCAAA
1955 AAAAAGAG
1 AAAAAGAG
1963 AAAAAGAG
1 AAAAAGAG
*
1971 AAAAAAAG
1 AAAAAGAG
*
1979 AAAAAAAG
1 AAAAAGAG
1987 AAAAA-AG
1 AAAAAGAG
1994 AAA
1 AAA
1997 TAGAAAGAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 5 0.15
8 28 0.85
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAGAG
Found at i:1980 original size:16 final size:16
Alignment explanation
Indices: 1953--2012 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 16
1943 AATTTCACCA
1953 AAAAAAAGAGAAAAAGAG
1 AAAAAAAGA-AAAAA-AG
1971 AAAAAAAGAAAAAAAG
1 AAAAAAAGAAAAAAAG
1987 -AAAAAAGAAATAGAAAG
1 AAAAAAAGAAA-A-AAAG
2004 AAGAAAAAG
1 AA-AAAAAG
2013 GAGACGTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
15 10 0.26
16 3 0.08
17 9 0.24
18 10 0.26
19 6 0.16
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAAAAAGAAAAAAAG
Found at i:1982 original size:25 final size:25
Alignment explanation
Indices: 1953--2012 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 25
1943 AATTTCACCA
*
1953 AAAAAAAGAGAAAAAGAGAA-AAAAAG
1 AAAAAAAGA-AAAAAGA-AATAGAAAG
1979 AAAAAAAGAAAAAAGAAATAGAAAG
1 AAAAAAAGAAAAAAGAAATAGAAAG
2004 AAGAAAAAG
1 AA-AAAAAG
2013 GAGACGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 2 0.06
25 14 0.45
26 15 0.48
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (25 bp):
AAAAAAAGAAAAAAGAAATAGAAAG
Found at i:3234 original size:147 final size:147
Alignment explanation
Indices: 3014--3628 Score: 595
Period size: 147 Copynumber: 4.2 Consensus size: 147
3004 TCTCATGCCC
* * ** * * *
3014 TAGAGATGTGAAGGGAAAGATTTAAGCCGTAATGGTGAATCTCATGCCCTAGAGATGTGAAGGGA
1 TAGAGATGTGATGGGAAAGATTAAAGCCGTAATGACGAATCTTATACCCTAGAGATGTGGAGGGA
* * * * * *
3079 AAGATTGAAGCCGCAAAGGCGAATCTTATACATTGGGGATATGGAGGGAAAGGTTGAAACCGTAA
66 AAGGTTGAAGCCGCAAAGACGAACCTTATACATTAGAGATATGGAGGGAAAGGTTGAAACCGCAA
* *
3144 CTACGAACCTTGTACCT
131 CGACGAACCTTATACCT
* * * * * * *
3161 TAGAGATATGATGGGAAAGATTAAAGCCGCAATGACAAATCTTGTACCCTAAAGATATGGAGAGA
1 TAGAGATGTGATGGGAAAGATTAAAGCCGTAATGACGAATCTTATACCCTAGAGATGTGGAGGGA
* * * * *
3226 AAGGTTGAAGTCG-AAACGACGAACCTTATA-ACCTAGAGATCTGGAGGGAAAGGTTGAACCCAC
66 AAGGTTGAAGCCGCAAA-GACGAACCTTATACA-TTAGAGATATGGAGGGAAAGGTTGAAACCGC
*
3289 AACGACAAACCTTATACCT
129 AACGACGAACCTTATACCT
* * * * *
3308 TAGAGATGTAATGAGAAAGATTGAAGCTGTAATGACGAATCTTATACCCTAGAGATGTAGAGGGA
1 TAGAGATGTGATGGGAAAGATTAAAGCCGTAATGACGAATCTTATACCCTAGAGATGTGGAGGGA
* * * * * *
3373 AAGGTTGAAGCCGCAACGACGAACCTTATACCTTATAGATGTAGAGGGAAAGGTTGAAGCCGCAA
66 AAGGTTGAAGCCGCAAAGACGAACCTTATACATTAGAGATATGGAGGGAAAGGTTGAAACCGCAA
*
3438 CGACGAACCTTATACGT
131 CGACGAACCTTATACCT
* * ** * * ** * *
3455 TAGAAATGTGATGGGAAAGATTGAAGTTGCAAAGGTGAATCTTATACCTTAGAGATGTAGAGGGA
1 TAGAGATGTGATGGGAAAGATTAAAGCCGTAATGACGAATCTTATACCCTAGAGATGTGGAGGGA
* * * * * * * * * *
3520 AAGGTTGAAGCTGTAACGATGAACCTTATACCTTAGAGATGTAGAGGAAAAGGTTGAAGCAGCAA
66 AAGGTTGAAGCCGCAAAGACGAACCTTATACATTAGAGATATGGAGGGAAAGGTTGAAACCGCAA
** *
3585 CGATAAATCTTATACCT
131 CGACGAACCTTATACCT
* ** *
3602 TAAAGATGTGAAAGGAAAGATTGAAGC
1 TAGAGATGTGATGGGAAAGATTAAAGC
3629 TGCAAAGGTA
Statistics
Matches: 389, Mismatches: 75, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
146 4 0.01
147 383 0.98
148 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (147 bp):
TAGAGATGTGATGGGAAAGATTAAAGCCGTAATGACGAATCTTATACCCTAGAGATGTGGAGGGA
AAGGTTGAAGCCGCAAAGACGAACCTTATACATTAGAGATATGGAGGGAAAGGTTGAAACCGCAA
CGACGAACCTTATACCT
Found at i:3398 original size:98 final size:97
Alignment explanation
Indices: 2958--3630 Score: 562
Period size: 98 Copynumber: 6.9 Consensus size: 97
2948 ACATTGAATC
* * * * * * *
2958 TATACCCTAGAGATGTGAAGCGAGAGATTGAAGTCGCAATGACGAATCTCATGCCCTAGAGATGT
1 TATACCCTAGAGATGTG-AGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCTTAGAGATGT
* * * * ** *
3023 GAAGGGAAAGATTTAAGCCGTAATGGTGAATCT
65 GAAGGGAAAGGTTGAAGCTGTAACGACGAACCT
* * * * * * * *
3056 CATGCCCTAGAGATGTGAAGGGAAAGATTGAAGCCGCAAAGGCGAATCTTATACATTGGGGATAT
1 TATACCCTAGAGATGTG-AGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCTTAGAGATGT
* * * *
3121 GGAGGGAAAGGTTGAAACCGTAACTACGAACCT
65 GAAGGGAAAGGTTGAAGCTGTAACGACGAACCT
* * * * * * * * * *
3154 TGTACCTTAGAGATATGATGGGAAAGATTAAAGCCGCAATGACAAATCTTGTACCCTAAAGATAT
1 TATACCCTAGAGATGTGA-GGGAAAGATTGAAGCCGCAACGACGAATCTTATACCTTAGAGATGT
* * *
3219 GGAGAGAAAGGTTGAAG-TCGAAACGACGAACCT
65 GAAGGGAAAGGTTGAAGCT-GTAACGACGAACCT
* * * * * * *
3252 TATAACCTAGAGATCTGGAGGGAAAGGTTGAACCCACAACGACAAACCTTATACCTTAGAGATGT
1 TATACCCTAGAGATGT-GAGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCTTAGAGATGT
* * * *
3317 -AATGAGAAAGATTGAAGCTGTAATGACGAATCT
65 GAA-GGGAAAGGTTGAAGCTGTAACGACGAACCT
* * *
3350 TATACCCTAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTATAGATGT
1 TATACCCTAGAGATGT-GAGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCTTAGAGATGT
* *
3415 -AGAGGGAAAGGTTGAAGCCGCAACGACGAACCT
65 GA-AGGGAAAGGTTGAAGCTGTAACGACGAACCT
** * ** * **
3448 TATACGTTAGAAATGTGATGGGAAAGATTGAAGTTGCAAAGGTGAATCTTATACCTTAGAGATGT
1 TATACCCTAGAGATGTGA-GGGAAAGATTGAAGCCGCAACGACGAATCTTATACCTTAGAGATGT
*
3513 -AGAGGGAAAGGTTGAAGCTGTAACGATGAACCT
65 GA-AGGGAAAGGTTGAAGCTGTAACGACGAACCT
* * * * ** *
3546 TATACCTTAGAGATGTAGAGGAAAAGGTTGAAGCAGCAACGATAAATCTTATACCTTAAAGATGT
1 TATACCCTAGAGATGT-GAGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCTTAGAGATGT
* *
3611 GAAAGGAAAGATTGAAGCTG
65 GAAGGGAAAGGTTGAAGCTG
3631 CAAAGGTAAA
Statistics
Matches: 465, Mismatches: 101, Indels: 18
0.80 0.17 0.03
Matches are distributed among these distances:
97 4 0.01
98 454 0.98
99 7 0.02
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (97 bp):
TATACCCTAGAGATGTGAGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCTTAGAGATGTG
AAGGGAAAGGTTGAAGCTGTAACGACGAACCT
Found at i:3548 original size:49 final size:49
Alignment explanation
Indices: 3063--3633 Score: 497
Period size: 49 Copynumber: 11.7 Consensus size: 49
3053 TCTCATGCCC
* * * * *
3063 TAGAGATGT-GAAGGGAAAGATTGAAGCCGCAAAGGCGAATCTTATACAT
1 TAGAGATGTAG-AGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCT
* * * * * * * *
3112 TGGGGATATGGAGGGAAAGGTTGAAACCGTAACTACGAACCTTGTACCT
1 TAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCT
* * * * * * * *
3161 TAGAGATAT-GATGGGAAAGATTAAAGCCGCAATGACAAATCTTGTACCC
1 TAGAGATGTAGA-GGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCT
* * * * * *
3210 TAAAGATATGGAGAGAAAGGTTGAAGTCGAAACGACGAACCTTATAACC-
1 TAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTAT-ACCT
* * * * *
3259 TAGAGATCTGGAGGGAAAGGTTGAACCCACAACGACAAACCTTATACCT
1 TAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCT
* * * * * * *
3308 TAGAGATGTA-ATGAGAAAGATTGAAGCTGTAATGACGAATCTTATACCC
1 TAGAGATGTAGA-GGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCT
3357 TAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCT
1 TAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCT
* *
3406 TATAGATGTAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACGT
1 TAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCT
* * ** * ** *
3455 TAGAAATGT-GATGGGAAAGATTGAAGTTGCAAAGGTGAATCTTATACCT
1 TAGAGATGTAGA-GGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCT
* * *
3504 TAGAGATGTAGAGGGAAAGGTTGAAGCTGTAACGATGAACCTTATACCT
1 TAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCT
* * ** *
3553 TAGAGATGTAGAGGAAAAGGTTGAAGCAGCAACGATAAATCTTATACCT
1 TAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCT
* * * *
3602 TAAAGATGT-GAAAGGAAAGATTGAAGCTGCAA
1 TAGAGATGTAG-AGGGAAAGGTTGAAGCCGCAA
3634 AGGTAAATCT
Statistics
Matches: 423, Mismatches: 89, Indels: 20
0.80 0.17 0.04
Matches are distributed among these distances:
48 9 0.02
49 405 0.96
50 9 0.02
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (49 bp):
TAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCT
Found at i:3643 original size:49 final size:48
Alignment explanation
Indices: 2952--3633 Score: 391
Period size: 49 Copynumber: 13.9 Consensus size: 48
2942 GAAAAAACAT
* * * * *
2952 TGAATC-TATACCCTAGAGATGTGAAGCGAGAGATTGAAG-TCGCAATGA
1 TGAATCTTATACCTTAGAGATGT-AAGGGAAAGGTTGAAGCT-GCAACGA
* * * * * * * * * *
3000 CGAATCTCATGCCCTAGAGATGTGAAGGGAAAGATTTAAGCCGTAATGG
1 TGAATCTTATACCTTAGAGATGT-AAGGGAAAGGTTGAAGCTGCAACGA
* * * * * * *
3049 TGAATCTCATGCCCTAGAGATGTGAAGGGAAAGATTGAAGCCGCAAAGG
1 TGAATCTTATACCTTAGAGATGT-AAGGGAAAGGTTGAAGCTGCAACGA
* * * * * * * * * *
3098 CGAATCTTATACATTGGGGATATGGAGGGAAAGGTTGAAACCGTAACTA
1 TGAATCTTATACCTTAGAGATGT-AAGGGAAAGGTTGAAGCTGCAACGA
* * * * * * * * *
3147 CGAACCTTGTACCTTAGAGATATGATGGGAAAGATTAAAGCCGCAATGA
1 TGAATCTTATACCTTAGAGATGT-AAGGGAAAGGTTGAAGCTGCAACGA
** * * * * * * *
3196 CAAATCTTGTACCCTAAAGATATGGAGAGAAAGGTTGAAG-TCGAAACGA
1 TGAATCTTATACCTTAGAGATGT-AAGGGAAAGGTTGAAGCT-GCAACGA
* * * * * **
3245 CGAACCTTATAACC-TAGAGATCTGGAGGGAAAGGTTGAACCCACAACGA
1 TGAATCTTAT-ACCTTAGAGATGT-AAGGGAAAGGTTGAAGCTGCAACGA
** * * * * *
3294 CAAACCTTATACCTTAGAGATGTAATGAGAAAGATTGAAGCTGTAATGA
1 TGAATCTTATACCTTAGAGATGTAA-GGGAAAGGTTGAAGCTGCAACGA
* * *
3343 CGAATCTTATACCCTAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGA
1 TGAATCTTATACCTTAGAGATGTA-AGGGAAAGGTTGAAGCTGCAACGA
* * * *
3392 CGAACCTTATACCTTATAGATGTAGAGGGAAAGGTTGAAGCCGCAACGA
1 TGAATCTTATACCTTAGAGATGTA-AGGGAAAGGTTGAAGCTGCAACGA
* * * * * * * * *
3441 CGAACCTTATACGTTAGAAATGTGATGGGAAAGATTGAAGTTGCAAAGG
1 TGAATCTTATACCTTAGAGATGT-AAGGGAAAGGTTGAAGCTGCAACGA
*
3490 TGAATCTTATACCTTAGAGATGTAGAGGGAAAGGTTGAAGCTGTAACGA
1 TGAATCTTATACCTTAGAGATGTA-AGGGAAAGGTTGAAGCTGCAACGA
* * *
3539 TGAACCTTATACCTTAGAGATGTAGAGGAAAAGGTTGAAGCAGCAACGA
1 TGAATCTTATACCTTAGAGATGTA-AGGGAAAGGTTGAAGCTGCAACGA
* * * *
3588 TAAATCTTATACCTTAAAGATGTGAAAGGAAAGATTGAAGCTGCAA
1 TGAATCTTATACCTTAGAGATGT-AAGGGAAAGGTTGAAGCTGCAA
3634 AGGTAAATCT
Statistics
Matches: 509, Mismatches: 114, Indels: 21
0.79 0.18 0.03
Matches are distributed among these distances:
48 10 0.02
49 493 0.97
50 6 0.01
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (48 bp):
TGAATCTTATACCTTAGAGATGTAAGGGAAAGGTTGAAGCTGCAACGA
Found at i:4033 original size:93 final size:95
Alignment explanation
Indices: 3934--4158 Score: 251
Period size: 99 Copynumber: 2.3 Consensus size: 95
3924 AACAGGTAGC
* *
3934 AGATCTCAATGTCTCTGAGGTTACAATGGAATGGAATGAAG-CACCAAATCCTATATCCCTAAAG
1 AGATCTCAATGTCTCTGAGGTTACAATGGAATGGAATGAAGACACAAAATCCTATACCCCTAAAG
**
3998 TTGCAATGGATCAGATCAAAATGA-GTAA-T
66 TTGCAATGGATCAGATCAAAACAATG-AAGT
* * *
4027 AGATCTCAATGTCCCTAAGGTTACAATGGAATGGAGTGAAGTTAAAACACAAAATCCTATACCCC
1 AGATCTCAATGTCTCTGAGGTTACAATGGAATGGAATGAAG-----ACACAAAATCCTATACCCC
* * * *
4092 TGAAGTTGTAATGGGTCAGATTAAAACAATGAAGT
61 TAAAGTTGCAATGGATCAGATCAAAACAATGAAGT
*
4127 AGATCTCAATGT-TCTTGAGGTTACAGTGGAAT
1 AGATCTCAATGTCTC-TGAGGTTACAATGGAAT
4159 AAAGAGAAGC
Statistics
Matches: 109, Mismatches: 14, Indels: 11
0.81 0.10 0.08
Matches are distributed among these distances:
93 38 0.35
99 42 0.39
100 29 0.27
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (95 bp):
AGATCTCAATGTCTCTGAGGTTACAATGGAATGGAATGAAGACACAAAATCCTATACCCCTAAAG
TTGCAATGGATCAGATCAAAACAATGAAGT
Found at i:4182 original size:100 final size:99
Alignment explanation
Indices: 3920--4183 Score: 238
Period size: 100 Copynumber: 2.7 Consensus size: 99
3910 ATGAAGTTGG
* ** * * * *
3920 TCAAAACAGGTAGCAGATCTCAATGTCTCTGAGGTTACAATGGAAT---G-GAA--TGAAGCACC
1 TCAAAACAAGTAATAGATCTCAATGTCCCTAAGGTTACAATGGAATAAAGAGAAGTTAAAACACC
*
3979 AAATCCTATATCCCTAAAGTTGCAATGGATCAGA
66 AAATCCTATACCCCTAAAGTTGCAATGGATCAGA
** ** * *
4013 TCAAAATGAGTAATAGATCTCAATGTCCCTAAGGTTACAATGGAATGGAGTGAAGTTAAAACACA
1 TCAAAACAAGTAATAGATCTCAATGTCCCTAAGGTTACAATGGAATAAAGAGAAGTTAAAACACC
* * *
4078 AAATCCTATACCCCTGAAGTTGTAATGGGTCAGA
66 AAATCCTATACCCCTAAAGTTGCAATGGATCAGA
* * * * * *
4112 TTAAAACAA-TGAAGTAGATCTCAATGTTCTTGAGGTTACAGTGGAATAAAGAGAAGCTT-CAAC
1 TCAAAACAAGT-AA-TAGATCTCAATGTCCCTAAGGTTACAATGGAATAAAGAGAAG-TTAAAAC
4175 ACCAAATCC
63 ACCAAATCC
4184 CATTTTCTTG
Statistics
Matches: 136, Mismatches: 26, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
93 39 0.29
96 1 0.01
97 3 0.02
98 1 0.01
99 44 0.32
100 46 0.34
101 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (99 bp):
TCAAAACAAGTAATAGATCTCAATGTCCCTAAGGTTACAATGGAATAAAGAGAAGTTAAAACACC
AAATCCTATACCCCTAAAGTTGCAATGGATCAGA
Done.