Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012411.1 Kokia drynarioides strain JFW-HI SEQ_127415, 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: 49438
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:474 original size:22 final size:22
Alignment explanation
Indices: 442--488 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
432 TTCAATAATG
442 AGTCGTCGTGTGGTTTTGTTTT
1 AGTCGTCGTGTGGTTTTGTTTT
*
464 AGTCGTTGTGTGGTTTTGTTTT
1 AGTCGTCGTGTGGTTTTGTTTT
486 AGT
1 AGT
489 TCATTGTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.06, C:0.06, G:0.32, T:0.55
Consensus pattern (22 bp):
AGTCGTCGTGTGGTTTTGTTTT
Found at i:2806 original size:2 final size:2
Alignment explanation
Indices: 2799--2832 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2789 GTGTTTTATC
*
2799 CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2833 ATATGTATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:12256 original size:73 final size:73
Alignment explanation
Indices: 12135--12278 Score: 261
Period size: 73 Copynumber: 2.0 Consensus size: 73
12125 CATCATCCAT
* *
12135 GGGCACCAACCAAGGTTTTCTCCTCACTATCTTTATGGTTTACGGATGTTTTCTTTACCAAAATG
1 GGGCACCAACCAAGGTTTTCTCCTCACTATCTTTACGGTTTACAGATGTTTTCTTTACCAAAATG
12200 TCTTCCCC
66 TCTTCCCC
*
12208 GGGCACCAACCAAGGTTTTCTCCTCACTATCTTTACGGTTTACAGATGTTTTCTTTACCAGAATG
1 GGGCACCAACCAAGGTTTTCTCCTCACTATCTTTACGGTTTACAGATGTTTTCTTTACCAAAATG
12273 TCTTCC
66 TCTTCC
12279 ACTGCAGGAA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (73 bp):
GGGCACCAACCAAGGTTTTCTCCTCACTATCTTTACGGTTTACAGATGTTTTCTTTACCAAAATG
TCTTCCCC
Found at i:13354 original size:102 final size:102
Alignment explanation
Indices: 13110--13355 Score: 280
Period size: 102 Copynumber: 2.4 Consensus size: 102
13100 AAGTCTATTT
**
13110 TATTAT-ACCTTGGGAAAAAGAGCCCTGCAATCACCACAATTAATCCAAATACATGGAGATACAC
1 TATTATAACCTTGGGAAAAAGAGCCCTGCAATCACCACAAAGAATCCAAATACATGGAGATACAC
* * * *
13174 AATTATGCAAAGCAAAGAATACAGAACTGTGAGCCTACA
66 AACTA--CAAAACAAAGAATACAAAACTATGAGCCTACA
* * * * * *
13213 TCATTATAACCTTGGAAAAAAGATCCATGTAATCGCCACAAAGAATCCAAATACATGGAGGTACA
1 T-ATTATAACCTTGGGAAAAAGAGCCCTGCAATCACCACAAAGAATCCAAATACATGGAGATACA
* * *
13278 CAACTA-AAAACAAAGGATATAAAACTATGAGTCTACA
65 CAACTACAAAACAAAGAATACAAAACTATGAGCCTACA
* **
13315 CTATTATAACCTTGGGGAAAAGAGCCCTGCAGCCACCACAA
1 -TATTATAACCTTGGGAAAAAGAGCCCTGCAATCACCACAA
13356 TTAGGGGAGA
Statistics
Matches: 117, Mismatches: 23, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
102 56 0.48
103 2 0.02
104 5 0.04
105 54 0.46
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (102 bp):
TATTATAACCTTGGGAAAAAGAGCCCTGCAATCACCACAAAGAATCCAAATACATGGAGATACAC
AACTACAAAACAAAGAATACAAAACTATGAGCCTACA
Found at i:21820 original size:59 final size:58
Alignment explanation
Indices: 21706--21822 Score: 153
Period size: 59 Copynumber: 2.0 Consensus size: 58
21696 CAATTTTTTT
*
21706 GTGTTGCCCATACAATGACCGACACCCCCATTTATCTGATAAAAAAATCAAAATTTTGA
1 GTGTTGCCCATACAATGACCGACACCCCCATTTATCAGATAAAAAAATC-AAATTTTGA
* * * * *
21765 GTGTTGGCCATGCAATGACCGACACCCCCCTTTTTATCAGATAAAAAATTCAATTTTT
1 GTGTTGCCCATACAATGACCGACA-CCCCC-ATTTATCAGATAAAAAAATCAAATTTT
21823 TGGTTCAGCC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 22 0.44
60 11 0.22
61 17 0.34
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (58 bp):
GTGTTGCCCATACAATGACCGACACCCCCATTTATCAGATAAAAAAATCAAATTTTGA
Found at i:21834 original size:59 final size:59
Alignment explanation
Indices: 21713--21849 Score: 145
Period size: 59 Copynumber: 2.3 Consensus size: 59
21703 TTTGTGTTGC
* **
21713 CCATACAATGACCGACACCCCCATTTATCTGATAAAAAAATCAAAATTTTGAGTGTTGG
1 CCATACAATGACCGACACCCCCATTTATCAGATAAAAAAATCAAAATTTTGAGTGTCAG
* * * **
21772 CCATGCAATGACCGACACCCCCCTTTTTATCAGATAAAAAATTCAATTTTTTG-GT-TCAG
1 CCATACAATGACCGACA-CCCCC-ATTTATCAGATAAAAAAATCAAAATTTTGAGTGTCAG
*
21831 CCATTAC-ATGACCAACACC
1 CCA-TACAATGACCGACACC
21850 AAAAAAATTT
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
58 2 0.03
59 30 0.46
60 9 0.14
61 24 0.37
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (59 bp):
CCATACAATGACCGACACCCCCATTTATCAGATAAAAAAATCAAAATTTTGAGTGTCAG
Found at i:21980 original size:62 final size:58
Alignment explanation
Indices: 21830--22173 Score: 298
Period size: 59 Copynumber: 5.7 Consensus size: 58
21820 TTTTGGTTCA
* * *
21830 GCCATTACATGACCAACACCAAAAAAATTTGGAATTTTTTTATCTGA-GAAAAGGGAGTGTCG
1 GCCATTGCATGGCCAACA-C-AAAAAATTT-GAA-TTTTTTATCTGATAAAAAGGG-GTGTCG
21892 GCCATTGCATGATGGCCGAAC-CAAAAAA-TTGAATTTTTTATCTGATAAAAAGGGGGGTGTCG
1 GCCATTGC---ATGGCC-AACACAAAAAATTTGAATTTTTTATCTGATAAAAA--GGGGTGTCG
* * * *
21954 ACCATTGCATGGCCAACACAAAAAAAATTTGAAAATTTTTTATCAGATAAATAGGGTTGTCG
1 GCCATTGCATGGCCAACAC--AAAAAATTTG--AATTTTTTATCTGATAAAAAGGGGTGTCG
* * ** * * *
22016 GCCATTGCATGGCCAACACCTAAAAATTTGATTTTTTTATCAAATAAATAGAGATGTCG
1 GCCATTGCATGGCCAACA-CAAAAAATTTGAATTTTTTATCTGATAAAAAGGGGTGTCG
* * * * * *
22075 GTCATTGTATGGCCAACACAAAAAAATTGTATTTTTTATCTGACAAAAAAGGGTTGTCG
1 GCCATTGCATGGCCAACACAAAAAATTTGAATTTTTTATCTGA-TAAAAAGGGGTGTCG
* ** *
22134 ACCATTGCATGGCCAACACCCAAAATTTGATTTTTTTATC
1 GCCATTGCATGGCCAACACAAAAAATTTGAATTTTTTATC
22174 AGATCAAATT
Statistics
Matches: 234, Mismatches: 33, Indels: 33
0.78 0.11 0.11
Matches are distributed among these distances:
58 22 0.09
59 91 0.39
60 12 0.05
61 22 0.09
62 50 0.21
63 10 0.04
64 19 0.08
65 5 0.02
66 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Consensus pattern (58 bp):
GCCATTGCATGGCCAACACAAAAAATTTGAATTTTTTATCTGATAAAAAGGGGTGTCG
Found at i:22053 original size:124 final size:117
Alignment explanation
Indices: 21831--22174 Score: 352
Period size: 124 Copynumber: 2.8 Consensus size: 117
21821 TTTGGTTCAG
* * * * *
21831 CCATTACATGACCAACACCAAAAAAATTTGGAATTTTTTTATCTGAGAAAAGGGAGTGTCGGCCA
1 CCATTGCATGGCCAACA-CAAAAAAATTT-GAAATTTTTTATCTGAAAAAAGGG-TTGTCGGCCA
* * * ** * *
21896 TTGCATGATGGCCGA-ACCAAAAAATTGAATTTTTTATCTGATAAAAAGGGGGGTGTCGA
63 TTGC---ATGGCCAACACCAAAAATTTGATTTTTTTATCAAATAAAAA--GAGATGTCGA
* *
21955 CCATTGCATGGCCAACACAAAAAAAATTTGAAAATTTTTTATCAGATAAATAGGGTTGTCGGCCA
1 CCATTGCATGGCCAACAC-AAAAAAATTTG-AAATTTTTTATCTGA-AAAAAGGGTTGTCGGCCA
* *
22020 TTGCATGGCCAACACCTAAAAATTTGATTTTTTTATCAAATAAATAGAGATGTCGG
63 TTGCATGGCCAACACC-AAAAATTTGATTTTTTTATCAAATAAAAAGAGATGTCGA
* * * *
22076 TCATTGTATGGCCAACACAAAAAAA-TTG-TATTTTTTATCTGACAAAAAAGGGTTGTCGACCAT
1 CCATTGCATGGCCAACACAAAAAAATTTGAAATTTTTTATCTG--AAAAAAGGGTTGTCGGCCAT
*
22139 TGCATGGCCAACACCCAAAATTTGATTTTTTTATCA
64 TGCATGGCCAACACCAAAAATTTGATTTTTTTATCA
22175 GATCAAATTT
Statistics
Matches: 190, Mismatches: 23, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
117 31 0.16
118 32 0.17
119 4 0.02
120 7 0.04
121 30 0.16
122 3 0.02
123 26 0.14
124 51 0.27
125 6 0.03
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (117 bp):
CCATTGCATGGCCAACACAAAAAAATTTGAAATTTTTTATCTGAAAAAAGGGTTGTCGGCCATTG
CATGGCCAACACCAAAAATTTGATTTTTTTATCAAATAAAAAGAGATGTCGA
Found at i:22694 original size:23 final size:22
Alignment explanation
Indices: 22669--22734 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 22
22659 TTATATCAAA
22669 AAACAAACTAATCATTTCTATT
1 AAACAAACTAATCATTTCTATT
** * *
22691 AAA-AATTTCATCAGTT-T-TT
1 AAACAAACTAATCATTTCTATT
22710 AAACAAACTAATCATTTCTATT
1 AAACAAACTAATCATTTCTATT
22732 AAA
1 AAA
22735 AATTTCATCA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 5 0.15
20 10 0.30
21 10 0.30
22 8 0.24
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (22 bp):
AAACAAACTAATCATTTCTATT
Found at i:22714 original size:41 final size:41
Alignment explanation
Indices: 22669--22751 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
22659 TTATATCAAA
*
22669 AAACAAACTAATCATTTCTATTAAAAATTTCATCAGTTTTT
1 AAACAAACTAATCATTTCTATTAAAAATTTCATCAATTTTT
22710 AAACAAACTAATCATTTCTATTAAAAATTTCATCAATTTTT
1 AAACAAACTAATCATTTCTATTAAAAATTTCATCAATTTTT
22751 A
1 A
22752 CTGTTAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.41
Consensus pattern (41 bp):
AAACAAACTAATCATTTCTATTAAAAATTTCATCAATTTTT
Found at i:22748 original size:22 final size:21
Alignment explanation
Indices: 22679--22744 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
22669 AAACAAACTA
22679 ATCATTTCTATTAAAAATTTC
1 ATCATTTCTATTAAAAATTTC
* ** *
22700 ATCAGTT-T-TTAAACAAACTA
1 ATCATTTCTATTAAA-AATTTC
22720 ATCATTTCTATTAAAAATTTC
1 ATCATTTCTATTAAAAATTTC
22741 ATCA
1 ATCA
22745 ATTTTTACTG
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 5 0.15
20 10 0.29
21 14 0.41
22 5 0.15
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.42
Consensus pattern (21 bp):
ATCATTTCTATTAAAAATTTC
Found at i:25594 original size:66 final size:65
Alignment explanation
Indices: 25484--25608 Score: 214
Period size: 66 Copynumber: 1.9 Consensus size: 65
25474 ATGAAAAGTC
* * *
25484 AGAGCAACATAGAACACAAGTGTGAATGGATGAAAATAAATTGGCAATATGAAAGAGGCTCTATT
1 AGAGCAACACAGAACACAAGTATGAATGGATGAAAATAAATTGGCAATATAAAAGAGGCTCTATT
25549 AGAGTCAACACAGAACACAAGTATGAATGGATGAAAATAAATTGGCAATATAAAAGAGGC
1 AGAG-CAACACAGAACACAAGTATGAATGGATGAAAATAAATTGGCAATATAAAAGAGGC
25609 CGACTTACAG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
65 4 0.07
66 52 0.93
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.19
Consensus pattern (65 bp):
AGAGCAACACAGAACACAAGTATGAATGGATGAAAATAAATTGGCAATATAAAAGAGGCTCTATT
Found at i:30131 original size:31 final size:32
Alignment explanation
Indices: 30088--30158 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
30078 GAAAAGTCGG
* *
30088 TATTTGAA-CACTTC-AAAAAAGATTTAATTTT
1 TATTT-AATCACTTCAAAAAAAGACTTAACTTT
*
30119 TATTTAATCACTTCAAAAAAAGACTTGACTTT
1 TATTTAATCACTTCAAAAAAAGACTTAACTTT
30151 TATTTAAT
1 TATTTAAT
30159 GATTTTGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 2 0.06
31 11 0.31
32 22 0.63
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (32 bp):
TATTTAATCACTTCAAAAAAAGACTTAACTTT
Found at i:30263 original size:47 final size:48
Alignment explanation
Indices: 30194--30290 Score: 169
Period size: 47 Copynumber: 2.0 Consensus size: 48
30184 TAAATAGAAA
*
30194 TAAAATCACTTATAATAATATTTATTATTTGTTTTAA-TTTTTTTAAT
1 TAAAATCACCTATAATAATATTTATTATTTGTTTTAATTTTTTTTAAT
*
30241 TAAAATCACCTATAATAATATTTGTTATTTGTTTTAATTTTTTTTAAT
1 TAAAATCACCTATAATAATATTTATTATTTGTTTTAATTTTTTTTAAT
30289 TA
1 TA
30291 TATTGGTATC
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 35 0.74
48 12 0.26
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (48 bp):
TAAAATCACCTATAATAATATTTATTATTTGTTTTAATTTTTTTTAAT
Found at i:35379 original size:30 final size:32
Alignment explanation
Indices: 35320--35390 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 32
35310 TTTTTATTAA
* *
35320 AAATATTTTTATTTAATTCTAATATATATTTTT
1 AAAT-TTTTTATTTAATTCTAAAATATATTTAT
*
35353 AAATTTTTTATTTGA-T-TAAAATATATTTAT
1 AAATTTTTTATTTAATTCTAAAATATATTTAT
35383 AAATTTTT
1 AAATTTTT
35391 AAAAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 20 0.57
31 1 0.03
32 10 0.29
33 4 0.11
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (32 bp):
AAATTTTTTATTTAATTCTAAAATATATTTAT
Found at i:35675 original size:25 final size:27
Alignment explanation
Indices: 35630--35685 Score: 82
Period size: 25 Copynumber: 2.1 Consensus size: 27
35620 TTTATATTTC
35630 AAATTTAAAAAACTTTACTTAAAATTA
1 AAATTTAAAAAACTTTACTTAAAATTA
35657 AAATTT-AAAAA--TTATCTTAAAATTA
1 AAATTTAAAAAACTTTA-CTTAAAATTA
35682 AAAT
1 AAAT
35686 ATATACATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 3 0.11
25 14 0.50
26 5 0.18
27 6 0.21
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (27 bp):
AAATTTAAAAAACTTTACTTAAAATTA
Found at i:44394 original size:43 final size:43
Alignment explanation
Indices: 44334--44421 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
44324 TGATACTTAT
*
44334 AATGAATGATTTTATTAATATATTTATAAATCGTAACATAATA
1 AATGAATGATTTTATTAATATACTTATAAATCGTAACATAATA
44377 AATGAATGATTTTATTAATATACTTATAAATCGTAACATAATA
1 AATGAATGATTTTATTAATATACTTATAAATCGTAACATAATA
44420 AA
1 AA
44422 ATTAAACATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.40
Consensus pattern (43 bp):
AATGAATGATTTTATTAATATACTTATAAATCGTAACATAATA
Found at i:46231 original size:9 final size:9
Alignment explanation
Indices: 46219--46247 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
46209 TATTTAGAAC
46219 TTTTAAAAT
1 TTTTAAAAT
46228 TTTTAAAA-
1 TTTTAAAAT
46236 TTTTAAAAT
1 TTTTAAAAT
46245 TTT
1 TTT
46248 AAATTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:46239 original size:8 final size:8
Alignment explanation
Indices: 46219--46250 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
46209 TATTTAGAAC
46219 TTTTAAAA
1 TTTTAAAA
46227 TTTTTAAAA
1 -TTTTAAAA
46236 TTTTAAAA
1 TTTTAAAA
46244 TTTTAAA
1 TTTTAAA
46251 TTAATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTTAAAA
Done.