Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014876.1 Kokia drynarioides strain JFW-HI SEQ_129919, 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: 73517
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:1724 original size:14 final size:15
Alignment explanation
Indices: 1697--1725 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1687 AAAAAGTAAT
1697 TTACAATCATCAAAA
1 TTACAATCATCAAAA
1712 TTACAAT-ATCAAAA
1 TTACAATCATCAAAA
1726 CTAAAGCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (15 bp):
TTACAATCATCAAAA
Found at i:2176 original size:35 final size:34
Alignment explanation
Indices: 2099--2198 Score: 128
Period size: 35 Copynumber: 2.9 Consensus size: 34
2089 GGTTGATATC
* *
2099 AAAATTCAAGGACCACGAACTAAAAATGAAAAAAA
1 AAAAGTCAAGGACCACGAACTAAAAAT-TAAAAAA
2134 AAAAGTCAAAGGACCACGAACTAAAAATTAAAAAA
1 AAAAGTC-AAGGACCACGAACTAAAAATTAAAAAA
* * *
2169 AAGAGTCAGGGACCACAAACCTAAAAATTA
1 AAAAGTCAAGGACCACGAA-CTAAAAATTA
2199 CATATTAGTA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
34 10 0.17
35 28 0.48
36 20 0.34
ACGTcount: A:0.59, C:0.16, G:0.13, T:0.12
Consensus pattern (34 bp):
AAAAGTCAAGGACCACGAACTAAAAATTAAAAAA
Found at i:2221 original size:55 final size:52
Alignment explanation
Indices: 2164--2269 Score: 121
Period size: 48 Copynumber: 2.1 Consensus size: 52
2154 CTAAAAATTA
* *
2164 AAAAAAAGAGTCAGGGACCACAAACCTAAAAATTACATATTAGTAATTATTAGT
1 AAAAAAA-A-TCAAGGACCACAAACCTAAAAATTAAATATTAGTAATTATTAGT
* * *
2218 ----AAAATTAAGGACCACGAACCTAAAATTTAAATATTAGTAATTATTAGT
1 AAAAAAAATCAAGGACCACAAACCTAAAAATTAAATATTAGTAATTATTAGT
2266 AAAA
1 AAAA
2270 TTAAGGACCA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
48 39 0.91
49 1 0.02
50 3 0.07
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.26
Consensus pattern (52 bp):
AAAAAAAATCAAGGACCACAAACCTAAAAATTAAATATTAGTAATTATTAGT
Found at i:2238 original size:48 final size:48
Alignment explanation
Indices: 2178--2283 Score: 185
Period size: 48 Copynumber: 2.2 Consensus size: 48
2168 AAAGAGTCAG
* *
2178 GGACCACAAACCTAAAAATTACATATTAGTAATTATTAGTAAAATTAA
1 GGACCACGAACCTAAAAATTAAATATTAGTAATTATTAGTAAAATTAA
*
2226 GGACCACGAACCTAAAATTTAAATATTAGTAATTATTAGTAAAATTAA
1 GGACCACGAACCTAAAAATTAAATATTAGTAATTATTAGTAAAATTAA
2274 GGACCACGAA
1 GGACCACGAA
2284 TAAATTATGT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.27
Consensus pattern (48 bp):
GGACCACGAACCTAAAAATTAAATATTAGTAATTATTAGTAAAATTAA
Found at i:3554 original size:23 final size:24
Alignment explanation
Indices: 3527--3582 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 24
3517 CAATTGAAAA
3527 TTTTAAATTTAAA-A-AAATATATT
1 TTTTAAATTTAAACACAAAT-TATT
*
3550 TTTTAATTTTTTAAACACAAATTATT
1 TTTTAA--ATTTAAACACAAATTATT
3576 TTTTAAA
1 TTTTAAA
3583 CATCAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
23 6 0.22
25 6 0.22
26 11 0.41
27 4 0.15
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTTAAATTTAAACACAAATTATT
Found at i:4043 original size:47 final size:46
Alignment explanation
Indices: 3938--4061 Score: 194
Period size: 47 Copynumber: 2.7 Consensus size: 46
3928 ATTGATAATT
3938 TTAAGGACCACAAATAAATTTATATGGTTTTCAAAAAAAATTAAAA
1 TTAAGGACCACAAATAAATTTATATGGTTTTCAAAAAAAATTAAAA
* * * *
3984 TTAAGGACCACAAACAAATTTTTATGGTCTTTTAAAAGAAATTAAAA
1 TTAAGGACCACAAATAAATTTATATGGT-TTTCAAAAAAAATTAAAA
*
4031 TTAAGGACCACAAATAAATTTATATAGTTTT
1 TTAAGGACCACAAATAAATTTATATGGTTTT
4062 TTTTCAAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
46 29 0.41
47 41 0.59
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (46 bp):
TTAAGGACCACAAATAAATTTATATGGTTTTCAAAAAAAATTAAAA
Found at i:4078 original size:47 final size:45
Alignment explanation
Indices: 3938--4081 Score: 159
Period size: 47 Copynumber: 3.1 Consensus size: 45
3928 ATTGATAATT
*
3938 TTAAGGACCACAAATAAATTTATATG-GTTTTCAAAAAAAATTAAAA
1 TTAAGGACCACAAATAAATTTATATGTCTTTTC-AAAAAAA-TAAAA
* *
3984 TTAAGGACCACAAACAAATTTTTATGGTCTTTT-AAAAGAAATTAAAA
1 TTAAGGACCACAAATAAATTTATAT-GTCTTTTCAAAA-AAA-TAAAA
*
4031 TTAAGGACCACAAATAAATTTATATAGTTTTTTTTCAAAAAAA-AAAA
1 TTAAGGACCACAAATAAATTTATAT-G--TCTTTTCAAAAAAATAAAA
4078 TTAA
1 TTAA
4082 TTTTATAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
46 27 0.32
47 42 0.49
48 4 0.05
49 8 0.09
50 4 0.05
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.33
Consensus pattern (45 bp):
TTAAGGACCACAAATAAATTTATATGTCTTTTCAAAAAAATAAAA
Found at i:8751 original size:26 final size:27
Alignment explanation
Indices: 8721--8771 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
8711 ATTTAATAAA
*
8721 TAAAAAATTATAAAGATATA-AATTAT
1 TAAAAAATTATAAAAATATACAATTAT
8747 TAAAAAATTATAAAAATATACAATT
1 TAAAAAATTATAAAAATATACAATT
8772 TAATTCCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (27 bp):
TAAAAAATTATAAAAATATACAATTAT
Found at i:10085 original size:2 final size:2
Alignment explanation
Indices: 10078--10114 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
10068 TTAACCTTTA
10078 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10115 GTGATTGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10311 original size:29 final size:28
Alignment explanation
Indices: 10275--10372 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 28
10265 ATTAGTAATG
10275 ATAAAATTATATTTTAATTTTTTTAAATA
1 ATAAAATTATATTTTAA-TTTTTTAAATA
* *
10304 ATAAAATTTTAATTTAATTTTTTAAA-A
1 ATAAAATTATATTTTAATTTTTTAAATA
* * *
10331 ATTATAAA-GATA-TAT-ATTATTTAAATA
1 A-TA-AAATTATATTTTAATTTTTTAAATA
10358 ATAAAATTATATTTT
1 ATAAAATTATATTTT
10373 TACTACCGTA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
25 3 0.05
26 14 0.25
27 8 0.14
28 13 0.23
29 18 0.32
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (28 bp):
ATAAAATTATATTTTAATTTTTTAAATA
Found at i:10361 original size:24 final size:21
Alignment explanation
Indices: 10329--10374 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 21
10319 AATTTTTTAA
*
10329 AAATTATAAAGATATATATTATTT
1 AAATAATAAA-AT-TATATT-TTT
10353 AAATAATAAAATTATATTTTT
1 AAATAATAAAATTATATTTTT
10374 A
1 A
10375 CTACCGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 6 0.29
23 2 0.10
24 9 0.43
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
AAATAATAAAATTATATTTTT
Found at i:11527 original size:31 final size:31
Alignment explanation
Indices: 11482--11546 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
11472 ATGACTTTTG
* * *
11482 ATTTGAGTATCAAATTAAACAATAAAATTAA
1 ATTTAAGTACCAAATCAAACAATAAAATTAA
* *
11513 ATTTAAGTACCAAATCAAATATTAAAATTAA
1 ATTTAAGTACCAAATCAAACAATAAAATTAA
11544 ATT
1 ATT
11547 CTGATATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.34
Consensus pattern (31 bp):
ATTTAAGTACCAAATCAAACAATAAAATTAA
Found at i:13554 original size:64 final size:64
Alignment explanation
Indices: 13477--13681 Score: 383
Period size: 64 Copynumber: 3.2 Consensus size: 64
13467 TCAAGTATGA
13477 GTCATTTCAAGTTGAGATTCAAGTAATTGTGAGTTTGGATTATTTCGAGCTTGAGTGATTTAGG
1 GTCATTTCAAGTTGAGATTCAAGTAATTGTGAGTTTGGATTATTTCGAGCTTGAGTGATTTAGG
13541 GTCATTTCAAGTTGAGATTCAAGTAATTGTGAGTTTGGATTATTTCGAGCTTGAGTGATTTAGG
1 GTCATTTCAAGTTGAGATTCAAGTAATTGTGAGTTTGGATTATTTCGAGCTTGAGTGATTTAGG
* * *
13605 GTCATTTCAAGTTGAGATTCAAGTAATTGTGAGTTCGGATTATTTCGAGTTTGAGTGATTTAAG
1 GTCATTTCAAGTTGAGATTCAAGTAATTGTGAGTTTGGATTATTTCGAGCTTGAGTGATTTAGG
13669 GTCATTTCAAGTT
1 GTCATTTCAAGTT
13682 CAAATCATTT
Statistics
Matches: 138, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 138 1.00
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.41
Consensus pattern (64 bp):
GTCATTTCAAGTTGAGATTCAAGTAATTGTGAGTTTGGATTATTTCGAGCTTGAGTGATTTAGG
Found at i:22920 original size:22 final size:21
Alignment explanation
Indices: 22876--22929 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
22866 AAAAAAAGTT
***
22876 AATTTATTTTTTCAAATTTAA
1 AATTTATTTTTTCAAAAAGAA
22897 AATTTATTATTTTCAAAAAGAA
1 AATTTATT-TTTTCAAAAAGAA
22919 AATTTATTTTT
1 AATTTATTTTT
22930 AAGTGAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (21 bp):
AATTTATTTTTTCAAAAAGAA
Found at i:34383 original size:52 final size:52
Alignment explanation
Indices: 34321--34423 Score: 152
Period size: 52 Copynumber: 2.0 Consensus size: 52
34311 TTAATAAAAA
* *
34321 ATTATATTAATCATTACTAGCTTAACAATTGAAATTTCCTTCCAAAATTTGG
1 ATTATATTAATCATTACTAGCTTAACAATTAAAATTACCTTCCAAAATTTGG
* * * *
34373 ATTATATTAATCGTTACTAGCTTAATAATTAAAATTACTTTCTAAAATTTG
1 ATTATATTAATCATTACTAGCTTAACAATTAAAATTACCTTCCAAAATTTG
34424 TTCACTTGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.43
Consensus pattern (52 bp):
ATTATATTAATCATTACTAGCTTAACAATTAAAATTACCTTCCAAAATTTGG
Found at i:34639 original size:174 final size:171
Alignment explanation
Indices: 34388--34766 Score: 505
Period size: 174 Copynumber: 2.2 Consensus size: 171
34378 ATTAATCGTT
* * *
34388 ACTAGCTTAATAATTAAAATTACTTTCTAAAATTTGTTCACTTGTGAACGAACTCAAATTCATAA
1 ACTAGCTTAATAATTAAAATTTCTTTCTAAAATTTATTCACTTGTGAACAAACTCAAATTCATAA
* * *
34453 TAAGGTCATTAAGCATTAATTCCATCACTCAATCAAAAACTTTTTACAGCTAAATAATA-CATCG
66 CAAGCTCATTAAGCATTAATTCCATCACTCAATCAAAAACTTTTTACAGCTAAACAATATC--CG
* * *
34517 CAAATTAAATTTCAGAGGATCAGTCAAGAGTTATACCAATCA-
129 CAAATCAAATTTCAGAGGATCAATCAAGAATTATACCAATCAC
*
34559 ACTAGCTTAA-AATTAAACTTTCTTTCTAAAATTTATTCACCGTTTTGTGAACAAA-TCCAAATT
1 ACTAGCTTAATAATTAAAATTTCTTTCTAAAATTTATTCA-C---TTGTGAACAAACT-CAAATT
* * *
34622 CATAACAAGCTCATTAAGCATTACTTCCATTACTCGATCAAAAACTTTTTACAGCTAAACAATAT
61 CATAACAAGCTCATTAAGCATTAATTCCATCACTCAATCAAAAACTTTTTACAGCTAAACAATAT
* * * *
34687 CCGCAAATCACATTTCAGAGGATTAATCAAGAATTATACTAATTAGC
126 CCGCAAATCAAATTTCAGAGGATCAATCAAGAATTATACCAATCA-C
34734 ACTAGCTTAATAATTAAAATTTCTTTCTAAAAT
1 ACTAGCTTAATAATTAAAATTTCTTTCTAAAAT
34767 AAAAAAATAA
Statistics
Matches: 181, Mismatches: 18, Indels: 13
0.85 0.08 0.06
Matches are distributed among these distances:
170 26 0.14
171 11 0.06
173 38 0.21
174 74 0.41
175 11 0.06
176 21 0.12
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (171 bp):
ACTAGCTTAATAATTAAAATTTCTTTCTAAAATTTATTCACTTGTGAACAAACTCAAATTCATAA
CAAGCTCATTAAGCATTAATTCCATCACTCAATCAAAAACTTTTTACAGCTAAACAATATCCGCA
AATCAAATTTCAGAGGATCAATCAAGAATTATACCAATCAC
Found at i:43391 original size:21 final size:20
Alignment explanation
Indices: 43367--43406 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
43357 ACTTAAATTT
43367 TAAATTAAAAAGTATATAAAC
1 TAAATTAAAAA-TATATAAAC
**
43388 TAAATTTTAAATATATAAA
1 TAAATTAAAAATATATAAA
43407 GAATGCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (20 bp):
TAAATTAAAAATATATAAAC
Found at i:50600 original size:18 final size:18
Alignment explanation
Indices: 50566--50600 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
50556 TTAAATTTTG
*
50566 TGAAAATTATAAGAATTT
1 TGAAAATTATAAAAATTT
*
50584 TGAAAATTTTAAAAATT
1 TGAAAATTATAAAAATT
50601 ATAATAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (18 bp):
TGAAAATTATAAAAATTT
Found at i:51793 original size:21 final size:21
Alignment explanation
Indices: 51767--51807 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
51757 TCAAAATGAC
51767 ATAATTTT-ACCTTTTAACTTA
1 ATAATTTTGA-CTTTTAACTTA
51788 ATAATTTTGACTTTTAACTT
1 ATAATTTTGACTTTTAACTT
51808 TAAAAAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (21 bp):
ATAATTTTGACTTTTAACTTA
Found at i:55542 original size:33 final size:37
Alignment explanation
Indices: 55480--55547 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 37
55470 CAAAATACAT
55480 TTTAAAATAAAATAATATAAATGTGTTAAAATTATTAA
1 TTTAAAATAAAATAATAT-AATGTGTTAAAATTATTAA
55518 TTTAAAATAAAA-AATAT-AT-T-TTAAAATTAT
1 TTTAAAATAAAATAATATAATGTGTTAAAATTAT
55548 ACAACTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 10 0.33
34 1 0.03
35 2 0.07
37 5 0.17
38 12 0.40
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (37 bp):
TTTAAAATAAAATAATATAATGTGTTAAAATTATTAA
Found at i:60292 original size:13 final size:14
Alignment explanation
Indices: 60276--60306 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
60266 CCAAACTTTG
60276 AACCTTAAA-CTCA
1 AACCTTAAATCTCA
60289 AACCTTAAATCTCA
1 AACCTTAAATCTCA
60303 AACC
1 AACC
60307 CGAACACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (14 bp):
AACCTTAAATCTCA
Found at i:62824 original size:21 final size:21
Alignment explanation
Indices: 62786--62825 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
62776 CGTGAAAATG
**
62786 GATTTAGAGTTTTTAAATTAA
1 GATTTAGAGTTTAAAAATTAA
*
62807 GATTTAGGGTTTAAAAATT
1 GATTTAGAGTTTAAAAATT
62826 TTAACTAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (21 bp):
GATTTAGAGTTTAAAAATTAA
Found at i:63164 original size:17 final size:17
Alignment explanation
Indices: 63121--63167 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
63111 AAAAGTTGAT
*
63121 TTATTCAAAT-TTTAAA
1 TTATTAAAATATTTAAA
*
63137 TTTTTAAAAATATTTAAA
1 TTATT-AAAATATTTAAA
63155 TTATTAAAATATT
1 TTATTAAAATATT
63168 AATATGTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 4 0.15
17 12 0.46
18 10 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATTAAAATATTTAAA
Found at i:68406 original size:16 final size:16
Alignment explanation
Indices: 68385--68416 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
68375 TATCCTCGTC
68385 CAAGAATTTGCTTGTT
1 CAAGAATTTGCTTGTT
*
68401 CAAGAATTTGTTTGTT
1 CAAGAATTTGCTTGTT
68417 AGCAAAGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.09, G:0.19, T:0.47
Consensus pattern (16 bp):
CAAGAATTTGCTTGTT
Done.