Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014902.1 Kokia drynarioides strain JFW-HI SEQ_129945, 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: 365448
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 23 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:346099 original size:52 final size:52
Alignment explanation
Indices: 345966--346100 Score: 173
Period size: 51 Copynumber: 2.6 Consensus size: 52
345956 GCTATAAACG
* * * * *
345966 AAAAGGTTCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGACT
1 AAAAGTTTCGATGACTAAGTGTCATCGTGAGTAAATAAATCCATGACGGACT
* * * *
346018 AAAGGTTT-GACGACTAAGTGTCATCGTGAGTAAATAAATCCATGATGGATT
1 AAAAGTTTCGATGACTAAGTGTCATCGTGAGTAAATAAATCCATGACGGACT
*
346069 AAAAGTTTCGATGACTCAGTGTCATCGTGAGT
1 AAAAGTTTCGATGACTAAGTGTCATCGTGAGT
346101 TTATGAATTC
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
51 43 0.61
52 27 0.39
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (52 bp):
AAAAGTTTCGATGACTAAGTGTCATCGTGAGTAAATAAATCCATGACGGACT
Found at i:353201 original size:51 final size:51
Alignment explanation
Indices: 353133--353311 Score: 207
Period size: 51 Copynumber: 3.5 Consensus size: 51
353123 GAAAAGGTTT
353133 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCC
* * * *
353184 GATGACTAAGTGTCATCGTGATTAAATGAATCCATGATAGATTAAAGGTCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCC
* * * * * * * **
353235 GATGATTCAGTGTCATCGTGAGCATATGAATTCCTATAAGAAACAAGAGGTCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTATGGATTAA-AGGTCC
353288 GATGACTATA-TGTCATCGTGAGTA
1 GATGACTA-AGTGTCATCGTGAGTA
353312 TTAAACAAAA
Statistics
Matches: 105, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
51 72 0.69
52 7 0.07
53 25 0.24
54 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (51 bp):
GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCC
Found at i:354524 original size:9 final size:9
Alignment explanation
Indices: 354512--354538 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
354502 AGGACAAAAA
354512 GGTGAAATT
1 GGTGAAATT
354521 GGTGAAATT
1 GGTGAAATT
354530 GGTGAAATT
1 GGTGAAATT
354539 ATATGTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (9 bp):
GGTGAAATT
Found at i:355073 original size:51 final size:51
Alignment explanation
Indices: 355004--355223 Score: 352
Period size: 51 Copynumber: 4.3 Consensus size: 51
354994 CGAAAGGGTT
*
355004 CGATGACTAAGTGTCATCGTGAGTGAATGAATCCTTTATGGATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTC
* * * *
355055 TGATGACTAAGTGTCATCGTGAGTGAATGAATCC-TTATGGATTAATGATC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTC
* *
355105 CGATAACTAAGTGTCATCGTGAGTAAATTAATCCTTTATGGATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTC
* *
355156 CGACGACTAAGTGTCATCGTGAGTAAATTAATCCTTTATGGATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTC
355207 CGATGACTAAGTGTCAT
1 CGATGACTAAGTGTCAT
355224 AATCAGTTTA
Statistics
Matches: 156, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
50 44 0.28
51 112 0.72
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (51 bp):
CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTC
Found at i:355189 original size:101 final size:102
Alignment explanation
Indices: 355004--355223 Score: 352
Period size: 101 Copynumber: 2.2 Consensus size: 102
354994 CGAAAGGGTT
* * *
355004 CGATGACTAAGTGTCATCGTGAGTGAATGAATCCTTTATGGATTAAAGGTCTGATGACTAAGTGT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCCGACGACTAAGTGT
* *
355069 CATCGTGAGTGAATGAATCC-TTATGGATTAATGATC
66 CATCGTGAGTAAATGAATCCTTTATGGATTAAAGATC
* *
355105 CGATAACTAAGTGTCATCGTGAGTAAATTAATCCTTTATGGATTAAAGGTCCGACGACTAAGTGT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCCGACGACTAAGTGT
* *
355170 CATCGTGAGTAAATTAATCCTTTATGGATTAAAGGTC
66 CATCGTGAGTAAATGAATCCTTTATGGATTAAAGATC
355207 CGATGACTAAGTGTCAT
1 CGATGACTAAGTGTCAT
355224 AATCAGTTTA
Statistics
Matches: 108, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
101 78 0.72
102 30 0.28
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (102 bp):
CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCCGACGACTAAGTGT
CATCGTGAGTAAATGAATCCTTTATGGATTAAAGATC
Found at i:356612 original size:20 final size:20
Alignment explanation
Indices: 356582--356633 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
356572 TTTTAATATA
*
356582 AATTT-TTAAATGTTATTGT
1 AATTTATTAAATGTTATTAT
*
356601 AATTTATTAAATTTTATTAT
1 AATTTATTAAATGTTATTAT
*
356621 TATTTATTTAAAT
1 AATTTA-TTAAAT
356634 TATTATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 5 0.18
20 17 0.61
21 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
AATTTATTAAATGTTATTAT
Found at i:357175 original size:23 final size:24
Alignment explanation
Indices: 357120--357178 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
357110 TTTAGATTTC
357120 AATTTC-ATTTAAAATTCATTTGA
1 AATTTCAATTTAAAATTCATTTGA
* *
357143 ACA-TTAAATTTAAATTTC-TTTGA
1 A-ATTTCAATTTAAAATTCATTTGA
357166 AATTTCAATTTAA
1 AATTTCAATTTAA
357179 TTTAAAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 1 0.03
23 18 0.60
24 11 0.37
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.47
Consensus pattern (24 bp):
AATTTCAATTTAAAATTCATTTGA
Found at i:357353 original size:19 final size:19
Alignment explanation
Indices: 357308--357345 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
357298 ATTTTAATTT
* *
357308 TAATTTCAAATTTAAACTA
1 TAATTTTAAATTCAAACTA
357327 TAATTTTAAATTCAAACTA
1 TAATTTTAAATTCAAACTA
357346 GTATTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATTTTAAATTCAAACTA
Found at i:357386 original size:36 final size:37
Alignment explanation
Indices: 357331--357402 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 37
357321 AAACTATAAT
*
357331 TTTAAATTCAAACTAGTATTTT-ATTTTGAAGTTAAA
1 TTTAAATTCAAACTAGTATTTTAATTTTGAAATTAAA
*
357367 TTTAAATTTAAAC-ATGTATTTTAATTTTGAAATTAA
1 TTTAAATTCAAACTA-GTATTTTAATTTTGAAATTAA
357403 TTTCAACTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
35 1 0.03
36 19 0.59
37 12 0.38
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (37 bp):
TTTAAATTCAAACTAGTATTTTAATTTTGAAATTAAA
Found at i:357492 original size:3 final size:3
Alignment explanation
Indices: 357484--357519 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
357474 AAAATTTGAA
357484 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
357520 GTATTTCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:361469 original size:45 final size:44
Alignment explanation
Indices: 361383--361469 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
361373 TTTTATCAAA
*
361383 CATGGCTGACACCAAAAAAAATATTTTTTTTATTAGCTAAAGAT
1 CATGGCTGACACCAAAAAAAATATTTTTTTTATTAGATAAAGAT
* * * *
361427 CATGGGTGACACCAAAAAAATTTTATTTTTTTATTTGATAAAG
1 CATGGCTGACACCAAAAAAAATAT-TTTTTTTATTAGATAAAG
361470 TGGGTGTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 21 0.57
45 16 0.43
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (44 bp):
CATGGCTGACACCAAAAAAAATATTTTTTTTATTAGATAAAGAT
Found at i:362140 original size:26 final size:21
Alignment explanation
Indices: 362091--362132 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
362081 ATTCTCAAAA
362091 TTTCGTGATGTGACAGAAAGC
1 TTTCGTGATGTGACAGAAAGC
362112 TTTCGTGATGTGACAGAAAGC
1 TTTCGTGATGTGACAGAAAGC
362133 ACAACTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (21 bp):
TTTCGTGATGTGACAGAAAGC
Found at i:362739 original size:4 final size:4
Alignment explanation
Indices: 362730--362764 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
362720 ATTGAAGGAA
*
362730 AAAG AAAG AAAA AAGAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AA-AG AAAG AAAG AAAG AAAG AA
362765 GAAGAAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.89
5 3 0.11
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:362807 original size:13 final size:13
Alignment explanation
Indices: 362728--362809 Score: 58
Period size: 13 Copynumber: 6.3 Consensus size: 13
362718 AAATTGAAGG
362728 AAAAAGAAAGAAA
1 AAAAAGAAAGAAA
*
362741 AAAGAGAAAG-AA
1 AAAAAGAAAGAAA
* *
362753 AGAAAGAAAGAAG
1 AAAAAGAAAGAAA
* * *
362766 AAGAAGGAAGAAG
1 AAAAAGAAAGAAA
*** *
362779 GGGAAGAAGGGAAA
1 AAAAAGAA-AGAAA
362793 AAAAAGAAAGAAA
1 AAAAAGAAAGAAA
362806 AAAA
1 AAAA
362810 TGTAATGTGT
Statistics
Matches: 51, Mismatches: 16, Indels: 4
0.72 0.23 0.06
Matches are distributed among these distances:
12 10 0.20
13 33 0.65
14 8 0.16
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAGAAA
Found at i:363189 original size:20 final size:21
Alignment explanation
Indices: 363148--363190 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
363138 TAATTTACTT
363148 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTTGTTAGTTAG
*
363169 TAATTTTATTTTGTT-GTTAG
1 TAATTTAATTTTGTTAGTTAG
363189 TA
1 TA
363191 GTAGTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (21 bp):
TAATTTAATTTTGTTAGTTAG
Found at i:363495 original size:16 final size:16
Alignment explanation
Indices: 363450--363499 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
363440 TAAATCTAGC
363450 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
*
363466 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
363480 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
363496 TAAT
1 TAAT
363500 ATCCCTATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 3 0.11
14 8 0.29
15 2 0.07
16 12 0.43
17 3 0.11
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:364866 original size:43 final size:43
Alignment explanation
Indices: 364784--364868 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
364774 ATTAACATGT
* *
364784 TAAATTATATTACTTGACTTGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTTGTATTAATATGCTTGCATGTTAC
*
364827 TAAATTATATTACTTTACTCT-TATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACT-TGTATTAATATGCTTG-CATGTTA
364869 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 3 0.08
43 33 0.89
44 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (43 bp):
TAAATTATATTACTTGACTTGTATTAATATGCTTGCATGTTAC
Done.