Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009287.1 Kokia drynarioides strain JFW-HI SEQ_123993, 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: 26406
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5452 original size:33 final size:33
Alignment explanation
Indices: 5415--5520 Score: 110
Period size: 33 Copynumber: 3.2 Consensus size: 33
5405 AAGGAGAAGA
5415 AAAACTTCAAAACAAAATAATGACATGACGGGC
1 AAAACTTCAAAACAAAATAATGACATGACGGGC
* **
5448 AAAACAGTATGAACAACAACAATAATGACA--AC-AAC
1 AAAAC--T-TCAA-AACAA-AATAATGACATGACGGGC
*
5483 AAAACTTCAAAACAAAATAATGACATGATGGGC
1 AAAACTTCAAAACAAAATAATGACATGACGGGC
5516 AAAAC
1 AAAAC
5521 AATACGAACA
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
30 10 0.17
31 5 0.09
32 4 0.07
33 12 0.21
35 7 0.12
36 5 0.09
37 5 0.09
38 10 0.17
ACGTcount: A:0.56, C:0.18, G:0.12, T:0.14
Consensus pattern (33 bp):
AAAACTTCAAAACAAAATAATGACATGACGGGC
Found at i:5472 original size:38 final size:36
Alignment explanation
Indices: 5425--5541 Score: 111
Period size: 38 Copynumber: 3.3 Consensus size: 36
5415 AAAACTTCAA
5425 AACAAAATAATGACATGACGGGCAAAACAGTATGAAC
1 AACAAAATAATGACATGACGGGCAAAACA-TATGAAC
** *
5462 AACAACAATAATGACA--AC-AACAAAAC-T-TCAA-
1 AACAA-AATAATGACATGACGGGCAAAACATATGAAC
* *
5493 AACAAAATAATGACATGATGGGCAAAACAATACGAAC
1 AACAAAATAATGACATGACGGGCAAAAC-ATATGAAC
5530 AACAACAATAAT
1 AACAA-AATAAT
5542 ATTAACATCT
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
30 10 0.16
31 5 0.08
32 4 0.06
33 7 0.11
35 7 0.11
36 4 0.06
37 10 0.16
38 16 0.25
ACGTcount: A:0.56, C:0.18, G:0.12, T:0.14
Consensus pattern (36 bp):
AACAAAATAATGACATGACGGGCAAAACATATGAAC
Found at i:5490 original size:68 final size:68
Alignment explanation
Indices: 5415--5541 Score: 227
Period size: 68 Copynumber: 1.9 Consensus size: 68
5405 AAGGAGAAGA
* *
5415 AAAACTTCAAAACAAAATAATGACATGACGGGCAAAACAGTATGAACAACAACAATAATGACAAC
1 AAAACTTCAAAACAAAATAATGACATGACGGGCAAAACAATACGAACAACAACAATAATGACAAC
5480 AAC
66 AAC
*
5483 AAAACTTCAAAACAAAATAATGACATGATGGGCAAAACAATACGAACAACAACAATAAT
1 AAAACTTCAAAACAAAATAATGACATGACGGGCAAAACAATACGAACAACAACAATAAT
5542 ATTAACATCT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.57, C:0.18, G:0.11, T:0.14
Consensus pattern (68 bp):
AAAACTTCAAAACAAAATAATGACATGACGGGCAAAACAATACGAACAACAACAATAATGACAAC
AAC
Found at i:5502 original size:30 final size:32
Alignment explanation
Indices: 5415--5507 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 32
5405 AAGGAGAAGA
**
5415 AAAACTTCAAAACAAAATAATGACATGACGGGC
1 AAAACTTCAAAACAAAATAATGACA-GACGAAC
*
5448 AAAACAGTATGAACAACAACAATAATGACA-AC-AAC
1 AAAAC--T-TCAA-AACAA-AATAATGACAGACGAAC
5483 AAAACTTCAAAACAAAATAATGACA
1 AAAACTTCAAAACAAAATAATGACA
5508 TGATGGGCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
30 10 0.20
31 5 0.10
32 3 0.06
33 6 0.12
35 7 0.14
36 5 0.10
37 5 0.10
38 10 0.20
ACGTcount: A:0.58, C:0.18, G:0.10, T:0.14
Consensus pattern (32 bp):
AAAACTTCAAAACAAAATAATGACAGACGAAC
Found at i:5970 original size:247 final size:248
Alignment explanation
Indices: 5516--6006 Score: 711
Period size: 247 Copynumber: 2.0 Consensus size: 248
5506 CATGATGGGC
* * * * * * *
5516 AAAACAATACGAACAACAACAATAATATTAACATCTTCTTGAGGGGGAGGTGGTGAAAAAGAGGG
1 AAAACAATACGAACAACAACAATAATAATAACATCTCCTTGAGCGAGAGATGCTGAAAAAGAAGG
* * * *
5581 GAGTCATTGAACATCTCCTTTTCTTAAGGCTAGCTCGTTGAGAAGCGTTGTCGGCTATCCAAGCA
66 AAATCATTAAACATCTCCTTTTCTTAAGGCTAGCTCGCTGAGAAGCGTTGTCGGCTATCCAAGCA
*
5646 AGTTTAACTTTTTCTCCCGTCATTGTTATTGCTATTGCTTTGTAAACCGCCTTTAACAATGGGTG
131 AGTTTAACTTTTTCTCCCGCCATTGTTATTGCTATTGCTTTGTAAACCGCCTTTAACAATGGGTG
5711 AAGGAGAGAACTGGTTTGCTTCAAAAGAGTGGCCAATGAGGCCTTTATAAATA
196 AAGGAGAGAACTGGTTTGCTTCAAAAGAGTGGCCAATGAGGCCTTTATAAATA
*
5764 AAAACAATAAC-AACAACAACAATAATAATAATATCTCCTTGAGCGAGAGATGCT-AAAGAAGAA
1 AAAACAAT-ACGAACAACAACAATAATAATAACATCTCCTTGAGCGAGAGATGCTGAAA-AAGAA
* * *
5827 GGAAATCGTTAAACATCTCCTTTTCTTAAGGCTAGCTCGCTGGGCAGCGTTGTC-GCTATCCAAG
64 GGAAATCATTAAACATCTCCTTTTCTTAAGGCTAGCTCGCTGAGAAGCGTTGTCGGCTATCCAAG
* * * * * *
5891 CAAGTTTAACTTTTTCTCCTGCCATT-TCTGTTGTTTTTGCTTTGTAAAGCGCTTTTAACAATGG
129 CAAGTTTAACTTTTTCTCCCGCCATTGT-TATTGCTATTGCTTTGTAAACCGCCTTTAACAATGG
* *
5955 GTGAAGGATAGAACTGGTTTGCTTCAAAAGAGTGGCTAATGAGGCCTTTATA
193 GTGAAGGAGAGAACTGGTTTGCTTCAAAAGAGTGGCCAATGAGGCCTTTATA
6007 TAGTTAGTGA
Statistics
Matches: 216, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
246 1 0.00
247 118 0.55
248 95 0.44
249 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (248 bp):
AAAACAATACGAACAACAACAATAATAATAACATCTCCTTGAGCGAGAGATGCTGAAAAAGAAGG
AAATCATTAAACATCTCCTTTTCTTAAGGCTAGCTCGCTGAGAAGCGTTGTCGGCTATCCAAGCA
AGTTTAACTTTTTCTCCCGCCATTGTTATTGCTATTGCTTTGTAAACCGCCTTTAACAATGGGTG
AAGGAGAGAACTGGTTTGCTTCAAAAGAGTGGCCAATGAGGCCTTTATAAATA
Found at i:13532 original size:7 final size:7
Alignment explanation
Indices: 13520--13544 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
13510 TATCTTCCTT
13520 TCCTTTC
1 TCCTTTC
13527 TCCTTTC
1 TCCTTTC
13534 TCCTTTC
1 TCCTTTC
13541 TCCT
1 TCCT
13545 CGCCCGATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (7 bp):
TCCTTTC
Found at i:15433 original size:14 final size:16
Alignment explanation
Indices: 15403--15434 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
15393 TTTAAAGCCC
15403 CCCAAAACAACTAAAA
1 CCCAAAACAACTAAAA
15419 CCCAAAA-AA-TAAAA
1 CCCAAAACAACTAAAA
15433 CC
1 CC
15435 TTTTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.62, C:0.31, G:0.00, T:0.06
Consensus pattern (16 bp):
CCCAAAACAACTAAAA
Found at i:18031 original size:15 final size:16
Alignment explanation
Indices: 18004--18033 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17994 TAAGGAAAAA
18004 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
18020 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
18034 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:20377 original size:22 final size:21
Alignment explanation
Indices: 20352--20403 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
20342 TTTCCTAGAC
20352 AAAAATAAATA-AATAAATAAA
1 AAAAATAAATAGAA-AAATAAA
*
20373 TAAAATAAGATAGAAAAATAAA
1 AAAAATAA-ATAGAAAAATAAA
20395 AAAAATAAA
1 AAAAATAAA
20404 AAAAATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 8 0.30
22 17 0.63
23 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (21 bp):
AAAAATAAATAGAAAAATAAA
Found at i:20380 original size:9 final size:9
Alignment explanation
Indices: 20354--20411 Score: 59
Period size: 9 Copynumber: 6.7 Consensus size: 9
20344 TCCTAGACAA
20354 AAAT-AAAT
1 AAATAAAAT
20362 AAAT-AAAT
1 AAATAAAAT
20370 AAATAAAAT
1 AAATAAAAT
*
20379 AAGATAGAA-
1 AA-ATAAAAT
*
20388 AAATAAAAA
1 AAATAAAAT
*
20397 AAATAAAAA
1 AAATAAAAT
20406 AAATAA
1 AAATAA
20412 TTGGGTTGCC
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
8 17 0.38
9 23 0.51
10 5 0.11
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.17
Consensus pattern (9 bp):
AAATAAAAT
Found at i:20404 original size:8 final size:8
Alignment explanation
Indices: 20352--20407 Score: 58
Period size: 8 Copynumber: 6.6 Consensus size: 8
20342 TTTCCTAGAC
20352 AAAAATAA
1 AAAAATAA
*
20360 ATAAATAA
1 AAAAATAA
*
20368 ATAAATAA
1 AAAAATAA
*
20376 AATAAGATAG
1 AA-AA-ATAA
20386 AAAAATAAA
1 AAAAAT-AA
20395 AAAAATAA
1 AAAAATAA
20403 AAAAA
1 AAAAA
20408 ATAATTGGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 25 0.61
9 11 0.27
10 5 0.12
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (8 bp):
AAAAATAA
Found at i:23165 original size:21 final size:22
Alignment explanation
Indices: 23141--23187 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
23131 CAATCTAAGG
23141 AAAAATAAAAGA-AATAAAATT
1 AAAAATAAAAGAGAATAAAATT
*
23162 AAAAATAAAAGAGAATAGAATT
1 AAAAATAAAAGAGAATAAAATT
23184 AAAA
1 AAAA
23188 GACATAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGAGAATAAAATT
Found at i:24048 original size:19 final size:19
Alignment explanation
Indices: 24005--24048 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
23995 ATAAACATAA
24005 ATTAAATAAAAAATTAAAT
1 ATTAAATAAAAAATTAAAT
* * * *
24024 AATAAATAATATATTGAAT
1 ATTAAATAAAAAATTAAAT
24043 ATTAAA
1 ATTAAA
24049 CCTAATATAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
ATTAAATAAAAAATTAAAT
Done.