Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011637.1 Kokia drynarioides strain JFW-HI SEQ_126628, 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: 113864
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:563 original size:33 final size:33
Alignment explanation
Indices: 465--564 Score: 123
Period size: 33 Copynumber: 3.0 Consensus size: 33
455 TCAACATAAG
*
465 TGATTGGAACATCTATCA-AGGCAGCTTCATCAA
1 TGATTGGAACATCTAT-AGAGGCAGCTTCATCAT
* *
498 TGATTGGAACATTTATCGCA-GCAGCTTCATCAT
1 TGATTGGAACATCTATAG-AGGCAGCTTCATCAT
* *
531 TGATTGGAACATCTCTAGGGGCAGCTTCATCAT
1 TGATTGGAACATCTATAGAGGCAGCTTCATCAT
564 T
1 T
565 TTGTTCGACT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
33 56 0.98
34 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (33 bp):
TGATTGGAACATCTATAGAGGCAGCTTCATCAT
Found at i:8042 original size:27 final size:25
Alignment explanation
Indices: 8012--8080 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 25
8002 TCATGCCATG
8012 TAAATTACATAATATATAAAAATAAA
1 TAAATTACATAA-ATATAAAAATAAA
*
8038 -ATAA--ACATAAATATAAATATAAA
1 TA-AATTACATAAATATAAAAATAAA
*
8061 TATATTACA-AAAGTATAAAA
1 TAAATTACATAAA-TATAAAA
8081 TGAGATGAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
23 13 0.37
24 10 0.29
25 10 0.29
26 2 0.06
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (25 bp):
TAAATTACATAAATATAAAAATAAA
Found at i:8053 original size:17 final size:18
Alignment explanation
Indices: 8027--8060 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
8017 TACATAATAT
8027 ATAAAAATAAA-ATAAAC
1 ATAAAAATAAATATAAAC
*
8044 ATAAATATAAATATAAA
1 ATAAAAATAAATATAAA
8061 TATATTACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAAAAATAAATATAAAC
Found at i:8061 original size:6 final size:6
Alignment explanation
Indices: 8020--8064 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
8010 TGTAAATTAC
* *
8020 ATAATAT ATAAAA ATAAA- ATAAAC ATAAAT ATAAAT ATAAAT ATA
1 ATAA-AT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATA
8065 TTACAAAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
5 5 0.14
6 26 0.74
7 4 0.11
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (6 bp):
ATAAAT
Found at i:13084 original size:3 final size:3
Alignment explanation
Indices: 13076--13104 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
13066 ATATCTACCA
13076 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
13105 AGTATCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:17419 original size:24 final size:25
Alignment explanation
Indices: 17376--17426 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
17366 TTTTTCTTGT
*
17376 ATAATAAATTTAATTAAATCTTAAA
1 ATAATAAAATTAATTAAATCTTAAA
*
17401 ATAATAAAATT-ATTGAATCTTAAA
1 ATAATAAAATTAATTAAATCTTAAA
17425 AT
1 AT
17427 TAAGACTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (25 bp):
ATAATAAAATTAATTAAATCTTAAA
Found at i:20023 original size:17 final size:17
Alignment explanation
Indices: 20001--20033 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
19991 CTCATTCTCC
20001 CTTCATTTTTCTTTTCT
1 CTTCATTTTTCTTTTCT
20018 CTTCATTTTTCTTTTC
1 CTTCATTTTTCTTTTC
20034 CTGCAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.70
Consensus pattern (17 bp):
CTTCATTTTTCTTTTCT
Found at i:23912 original size:19 final size:19
Alignment explanation
Indices: 23888--23943 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
23878 GAAGAAAGTG
*
23888 AGTAAAAATTTTTGAGAAA
1 AGTAAAAAGTTTTGAGAAA
* *
23907 AGTAAAAAGGTTTGGGAAA
1 AGTAAAAAGTTTTGAGAAA
23926 AGTAAAAAAGTTTTGAGA
1 AGT-AAAAAGTTTTGAGA
23944 TTTGGGGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (19 bp):
AGTAAAAAGTTTTGAGAAA
Found at i:33860 original size:23 final size:23
Alignment explanation
Indices: 33834--33880 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
33824 TTTTGTGAAC
33834 ATGAATCTTGTTTTTATTAAATA
1 ATGAATCTTGTTTTTATTAAATA
33857 ATGAATCTTGTTTTTATTAAATA
1 ATGAATCTTGTTTTTATTAAATA
33880 A
1 A
33881 GTAGAAGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (23 bp):
ATGAATCTTGTTTTTATTAAATA
Found at i:35371 original size:56 final size:56
Alignment explanation
Indices: 35298--35412 Score: 194
Period size: 56 Copynumber: 2.1 Consensus size: 56
35288 GTGTAACCAT
* * * *
35298 TATTTGTAAGAATTTTTAAATCAGTTAAAATTAAATCATCATATGTAATATGTTAG
1 TATTTATAAGAATTTTTAAATCAGTTAAAATCAAATCATCATACGTAATATCTTAG
35354 TATTTATAAGAATTTTTAAATCAGTTAAAATCAAATCATCATACGTAATATCTTAG
1 TATTTATAAGAATTTTTAAATCAGTTAAAATCAAATCATCATACGTAATATCTTAG
35410 TAT
1 TAT
35413 AAGAAAGTAG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.42
Consensus pattern (56 bp):
TATTTATAAGAATTTTTAAATCAGTTAAAATCAAATCATCATACGTAATATCTTAG
Found at i:47225 original size:24 final size:25
Alignment explanation
Indices: 47177--47225 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
47167 AAAATTATAG
* *
47177 CTTTTTGATAAAGATGGCATCTTTT
1 CTTTTGGATAAAGATGACATCTTTT
*
47202 CTTTTGGATAAGGATGACAT-TTTT
1 CTTTTGGATAAAGATGACATCTTTT
47226 GTCATGGTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.47
Consensus pattern (25 bp):
CTTTTGGATAAAGATGACATCTTTT
Found at i:65278 original size:20 final size:20
Alignment explanation
Indices: 65242--65291 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
65232 TTATTAAGCT
*
65242 TTAATTAACCACTTTTA-ATC
1 TTAATTAAACACTTTTATA-C
65262 TTAATTAAAC-CTATTTATAC
1 TTAATTAAACACT-TTTATAC
65282 TTAATATAAA
1 TTAAT-TAAA
65292 TCATGCTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATTAAACACTTTTATAC
Found at i:67572 original size:51 final size:51
Alignment explanation
Indices: 67506--67614 Score: 164
Period size: 51 Copynumber: 2.1 Consensus size: 51
67496 ATTATGTGAA
* * * **
67506 AAAAAAATTAAAATAATTAAATGATAATTTTATAATTTTTTATAATTAAAT
1 AAAAAAATAAAAATAATTAAATAATAATTTTATAACTTTCCATAATTAAAT
*
67557 AAAAAAATAAAAATAATTAAATAATATTTTTATAACTTTCCATAATTAAAT
1 AAAAAAATAAAAATAATTAAATAATAATTTTATAACTTTCCATAATTAAAT
67608 AAAAAAA
1 AAAAAAA
67615 AATGATAGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.38
Consensus pattern (51 bp):
AAAAAAATAAAAATAATTAAATAATAATTTTATAACTTTCCATAATTAAAT
Found at i:82253 original size:28 final size:29
Alignment explanation
Indices: 82229--82300 Score: 119
Period size: 28 Copynumber: 2.4 Consensus size: 29
82219 ATTAAAATTA
82229 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-TATTT-AAAAAAATAAT
82260 TTTAATAATTTTATATTT-AAAAAATAAT
1 TTTAATAATTTTATATTTAAAAAAATAAT
82288 TTTAATAATTTTA
1 TTTAATAATTTTA
82301 AAATAATTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
28 23 0.56
30 5 0.12
31 13 0.32
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
TTTAATAATTTTATATTTAAAAAAATAAT
Found at i:82287 original size:19 final size:20
Alignment explanation
Indices: 82263--82309 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
82253 AAATAATTTT
82263 AATAATTTT-AT-ATTTAAAA
1 AATAATTTTAATAATTT-AAA
*
82282 AATAATTTTAATAATTTTAA
1 AATAATTTTAATAATTTAAA
82302 AATAATTT
1 AATAATTT
82310 GCTGACATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 9 0.36
20 12 0.48
21 4 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATAATTTTAATAATTTAAA
Found at i:94096 original size:23 final size:23
Alignment explanation
Indices: 94042--94099 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
94032 AGTTTTCCTT
94042 TTTTTGTTCTTTCTTTCTTCCTCCC
1 TTTTT-TTCTTTCTTTCTT-CTCCC
*
94067 -TTCTTTCTTTCCTTTCTT-TCCC
1 TTTTTTTCTTT-CTTTCTTCTCCC
94089 TTTTTTTCTTT
1 TTTTTTTCTTT
94100 GTTGTCTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 4 0.14
23 15 0.52
24 10 0.34
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTTTTCTTTCTTTCTTCTCCC
Found at i:94727 original size:13 final size:13
Alignment explanation
Indices: 94709--94747 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
94699 TTCTTTTACA
*
94709 ATTAACCTTCAAT
1 ATTAACCTCCAAT
94722 ATTAACCTCCAAT
1 ATTAACCTCCAAT
94735 ATTAACCTCCAAT
1 ATTAACCTCCAAT
94748 GTCACAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.33
Consensus pattern (13 bp):
ATTAACCTCCAAT
Found at i:98789 original size:18 final size:18
Alignment explanation
Indices: 98766--98811 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
98756 CTATTTATAT
*
98766 TATTGAATTTTTTAATAA
1 TATTGAATTTTATAATAA
*
98784 TATTGAATATTTATATTAA
1 TATTGAAT-TTTATAATAA
*
98803 AATTGAATT
1 TATTGAATT
98812 ATTAATGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (18 bp):
TATTGAATTTTATAATAA
Found at i:100476 original size:45 final size:45
Alignment explanation
Indices: 100390--100477 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
100380 GCGAATATGT
* * *
100390 TCTTCTCAGTTTTGCAAACATCTATGTGTTTTCTTGTTCTTATTA
1 TCTTCTCAGTTTTGCAAACATCAACGTGTTTTCTTGATCTTATTA
* *
100435 TCTTCTCAGTTTTGCGAGCATCAACGTGTTTTCCTT-ATCTTAT
1 TCTTCTCAGTTTTGCAAACATCAACGTGTTTT-CTTGATCTTAT
100478 ATTTTCTTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
45 34 0.92
46 3 0.08
ACGTcount: A:0.17, C:0.20, G:0.12, T:0.50
Consensus pattern (45 bp):
TCTTCTCAGTTTTGCAAACATCAACGTGTTTTCTTGATCTTATTA
Found at i:103190 original size:22 final size:22
Alignment explanation
Indices: 103165--103237 Score: 94
Period size: 22 Copynumber: 3.3 Consensus size: 22
103155 TTAGTTGATT
103165 GTTGTTTCTTTATCAATTTATG
1 GTTGTTTCTTTATCAATTTATG
* * * *
103187 GTTGTTTCATTT-TTAGTTGATT
1 GTTGTTTC-TTTATCAATTTATG
103209 GTTGTTTCTTTATCAATTTATG
1 GTTGTTTCTTTATCAATTTATG
103231 GTTGTTT
1 GTTGTTT
103238 TAGTTTCATA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 3 0.07
22 35 0.85
23 3 0.07
ACGTcount: A:0.15, C:0.07, G:0.16, T:0.62
Consensus pattern (22 bp):
GTTGTTTCTTTATCAATTTATG
Found at i:103196 original size:44 final size:44
Alignment explanation
Indices: 103148--103237 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
103138 ATTATCCAAA
103148 TTCATTTTTAGTTGATTGTTGTTTCTTTATCAATTTATGGTTGT
1 TTCATTTTTAGTTGATTGTTGTTTCTTTATCAATTTATGGTTGT
103192 TTCATTTTTAGTTGATTGTTGTTTCTTTATCAATTTATGGTTGT
1 TTCATTTTTAGTTGATTGTTGTTTCTTTATCAATTTATGGTTGT
103236 TT
1 TT
103238 TAGTTTCATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.16, C:0.07, G:0.16, T:0.62
Consensus pattern (44 bp):
TTCATTTTTAGTTGATTGTTGTTTCTTTATCAATTTATGGTTGT
Found at i:103220 original size:19 final size:20
Alignment explanation
Indices: 103153--103219 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 20
103143 CCAAATTCAT
103153 TTTTAGTTGATTGTTGTTTC
1 TTTTAGTTGATTGTTGTTTC
* * *
103173 TTTATCAATTTATGGTTGTTTC
1 TTT-T-AGTTGATTGTTGTTTC
103195 ATTTTTAGTTGATTGTTGTTTC
1 --TTTTAGTTGATTGTTGTTTC
103217 TTT
1 TTT
103220 ATCAATTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
20 6 0.16
21 1 0.03
22 26 0.70
23 1 0.03
24 3 0.08
ACGTcount: A:0.13, C:0.06, G:0.16, T:0.64
Consensus pattern (20 bp):
TTTTAGTTGATTGTTGTTTC
Found at i:103448 original size:61 final size:61
Alignment explanation
Indices: 103340--103457 Score: 148
Period size: 61 Copynumber: 1.9 Consensus size: 61
103330 TTAATTACCG
* ** *
103340 TTTGATTTTATATCTTTATTTTGACAAAAGAAATTGATTTAAATAACTAAGTATTTTCTTC
1 TTTGATTTTATATCTTTATTTGGACAAAAGAAACAGATGTAAATAACTAAGTATTTTCTTC
* * * *
103401 TTTGATTTTATATCTTTGTTATGGA-AAAAGAAACAGATGTCAGTAACTGAGTATTTT
1 TTTGATTTTATATCTTTATT-TGGACAAAAGAAACAGATGTAAATAACTAAGTATTTT
103458 AACAGATTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
61 45 0.94
62 3 0.06
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.46
Consensus pattern (61 bp):
TTTGATTTTATATCTTTATTTGGACAAAAGAAACAGATGTAAATAACTAAGTATTTTCTTC
Found at i:108749 original size:31 final size:31
Alignment explanation
Indices: 108713--108775 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
108703 AATATTTTTT
*
108713 AAATTAAAACTGAATAATAAAATTCAATCAA
1 AAATTAAAACTGAATAACAAAATTCAATCAA
** * *
108744 AAATTAAATTTTAATGACAAAATTCAATCAA
1 AAATTAAAACTGAATAACAAAATTCAATCAA
108775 A
1 A
108776 CAAAAGTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.29
Consensus pattern (31 bp):
AAATTAAAACTGAATAACAAAATTCAATCAA
Found at i:109858 original size:22 final size:22
Alignment explanation
Indices: 109828--109890 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
109818 AGTTATTTCA
*
109828 TTTAGTTTTA-TGCTTTATTTATT
1 TTTAGTTTTATTG--TTAGTTATT
*
109851 TTTATTTTTATTGTTAGTTATT
1 TTTAGTTTTATTGTTAGTTATT
109873 TTTA-TTTTATT-TTA-TTAT
1 TTTAGTTTTATTGTTAGTTAT
109891 GCACTGTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 4 0.11
20 3 0.08
21 7 0.19
22 12 0.32
23 9 0.24
24 2 0.05
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (22 bp):
TTTAGTTTTATTGTTAGTTATT
Found at i:109887 original size:16 final size:16
Alignment explanation
Indices: 109841--109888 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
109831 AGTTTTATGC
109841 TTTA-TTTATTTTTATT
1 TTTATTTTA-TTTTATT
*
109857 TTTATTGTTA-GTTATT
1 TTTATT-TTATTTTATT
109873 TTTATTTTATTTTATT
1 TTTATTTTATTTTATT
109889 ATGCACTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 3 0.11
16 20 0.74
17 1 0.04
18 3 0.11
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (16 bp):
TTTATTTTATTTTATT
Found at i:109959 original size:21 final size:23
Alignment explanation
Indices: 109924--109965 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
109914 CGATTGTTTT
*
109924 TTTTATGTTTTTATT-TTATTTA
1 TTTTATGTTTATATTATTATTTA
109946 TTTT-TGTTTATATTATTATT
1 TTTTATGTTTATATTATTATT
109966 AGTATGCTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (23 bp):
TTTTATGTTTATATTATTATTTA
Done.