Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011746.1 Kokia drynarioides strain JFW-HI SEQ_126740, 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: 39027
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Warning! 124 characters in sequence are not A, C, G, or T
Found at i:5195 original size:58 final size:59
Alignment explanation
Indices: 5131--5251 Score: 165
Period size: 59 Copynumber: 2.1 Consensus size: 59
5121 AAAAAGAGTT
* *
5131 GTTTATGAGTG-TTATTTAGGAATAAAATTATATTT-GGCTTTCAAAATATTTAGGTTTA
1 GTTTATGAGTGTTTATTTAAGAATAAAATTATATTTGGGC-TTAAAAATATTTAGGTTTA
* * * *
5189 GTTTATGAGTGTTTTTTTAAGAATGAAATTATATTTGGGCTTAAAAATATTTGGGTTTG
1 GTTTATGAGTGTTTATTTAAGAATAAAATTATATTTGGGCTTAAAAATATTTAGGTTTA
5248 GTTT
1 GTTT
5252 GTTGATGAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 11 0.20
59 41 0.75
60 3 0.05
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (59 bp):
GTTTATGAGTGTTTATTTAAGAATAAAATTATATTTGGGCTTAAAAATATTTAGGTTTA
Found at i:6693 original size:17 final size:18
Alignment explanation
Indices: 6666--6704 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
6656 ATTTAGAATT
6666 TTTTTTAAAAAATATAAA
1 TTTTTTAAAAAATATAAA
6684 TTTTTT-AAAAATATAAA
1 TTTTTTAAAAAATATAAA
6701 TTTT
1 TTTT
6705 AAAATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTTTAAAAAATATAAA
Found at i:6731 original size:19 final size:19
Alignment explanation
Indices: 6707--6746 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
6697 TAAATTTTAA
6707 AATTTTAATAAA-TATTTTG
1 AATTTTAA-AAATTATTTTG
6726 AATTTTAAAAATTATTTTG
1 AATTTTAAAAATTATTTTG
6745 AA
1 AA
6747 CTTGTTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
AATTTTAAAAATTATTTTG
Found at i:9402 original size:7 final size:7
Alignment explanation
Indices: 9390--9430 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
9380 CTGTTAACAT
9390 TCACCTC
1 TCACCTC
9397 TCACCTC
1 TCACCTC
*
9404 TCATCTC
1 TCACCTC
9411 TCACCTC
1 TCACCTC
*
9418 TCA-CTT
1 TCACCTC
9424 TCACCTC
1 TCACCTC
9431 ACTCTTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.15, C:0.51, G:0.00, T:0.34
Consensus pattern (7 bp):
TCACCTC
Found at i:15696 original size:31 final size:31
Alignment explanation
Indices: 15654--15719 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 31
15644 AAAGGGGTCT
*
15654 AAAATATTATTTTCCAGTTTTTAAGGGACCCAAA
1 AAAATA-T-TTTTCCAATTTTTAA-GGACCCAAA
**
15688 AAAATATTTTTTTAATTTTTAAGGACCCAAA
1 AAAATATTTTTCCAATTTTTAAGGACCCAAA
15719 A
1 A
15720 TTGTTTTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 10 0.34
32 12 0.41
33 1 0.03
34 6 0.21
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (31 bp):
AAAATATTTTTCCAATTTTTAAGGACCCAAA
Found at i:23308 original size:50 final size:51
Alignment explanation
Indices: 23249--23353 Score: 167
Period size: 51 Copynumber: 2.1 Consensus size: 51
23239 GTAGCTATAA
* *
23249 ATCATTTGTTGATA-TTAAGTGCCCATGTGTTGTATGTATCAAGATAGGGT
1 ATCATTTGTTCATATTTAAGTGCCCATGTGTTGCATGTATCAAGATAGGGT
* *
23299 ATCATTTGTTCATATTTAAGTGTCCATTTGTTGCATGTATCAAGATAGGGT
1 ATCATTTGTTCATATTTAAGTGCCCATGTGTTGCATGTATCAAGATAGGGT
23350 ATCA
1 ATCA
23354 AAACCAGCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
50 13 0.26
51 37 0.74
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (51 bp):
ATCATTTGTTCATATTTAAGTGCCCATGTGTTGCATGTATCAAGATAGGGT
Found at i:26468 original size:14 final size:14
Alignment explanation
Indices: 26434--26509 Score: 55
Period size: 15 Copynumber: 5.2 Consensus size: 14
26424 ACAATACGTA
* *
26434 AAAATTAAATAAAT
1 AAAATTATATATAT
26448 CAAAATTATATATAT
1 -AAAATTATATATAT
* *
26463 AAAATTACATAAAAT
1 AAAATTATAT-ATAT
* *
26478 CAAATTTTATATATAA
1 -AAA-ATTATATATAT
26494 AAAATTATATAT-T
1 AAAATTATATATAT
26507 AAA
1 AAA
26510 CAAAAATTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
13 3 0.06
14 17 0.35
15 18 0.38
16 5 0.10
17 5 0.10
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATTATATATAT
Found at i:26475 original size:29 final size:29
Alignment explanation
Indices: 26434--26495 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
26424 ACAATACGTA
26434 AAAATTAAAT-AAATCAAAATTATATATAT
1 AAAATTAAATAAAATC-AAATTATATATAT
* *
26463 AAAATTACATAAAATCAAATTTTATATAT
1 AAAATTAAATAAAATCAAATTATATATAT
26492 AAAA
1 AAAA
26496 AATTATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (29 bp):
AAAATTAAATAAAATCAAATTATATATAT
Found at i:26491 original size:31 final size:29
Alignment explanation
Indices: 26433--26526 Score: 91
Period size: 33 Copynumber: 3.0 Consensus size: 29
26423 AACAATACGT
26433 AAAAATTAAATAAATCAAAATTATATATA
1 AAAAATTAAATAAATCAAAATTATATATA
* * *
26462 TAAAATTACATAAAATCAAATTTTATATATA
1 AAAAATTAAAT-AAATCAAA-ATTATATATA
26493 AAAAATTATATATTAAA-CAAAAATTTATATATA
1 AAAAATTA-A-A-TAAATC-AAAA-TTATATATA
26526 A
1 A
26527 TTTTAAAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
29 9 0.17
30 8 0.15
31 16 0.31
32 1 0.02
33 17 0.33
34 1 0.02
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAAATTAAATAAATCAAAATTATATATA
Found at i:26520 original size:33 final size:31
Alignment explanation
Indices: 26433--26526 Score: 104
Period size: 31 Copynumber: 3.0 Consensus size: 31
26423 AACAATACGT
*
26433 AAAAATTAAAT-AAATCAAAA-TTATATATA
1 AAAAATTACATAAAATCAAAATTTATATATA
* *
26462 TAAAATTACATAAAATCAAATTTTATATATA
1 AAAAATTACATAAAATCAAAATTTATATATA
*
26493 AAAAATTATATATTAAA-CAAAAATTTATATATA
1 AAAAATTACATA--AAATC-AAAATTTATATATA
26526 A
1 A
26527 TTTTAAAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
29 9 0.17
30 8 0.15
31 19 0.35
32 1 0.02
33 17 0.31
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (31 bp):
AAAAATTACATAAAATCAAAATTTATATATA
Found at i:31573 original size:21 final size:22
Alignment explanation
Indices: 31547--31588 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
31537 ACTGTCTCTG
31547 TAAATT-TAAAAATAAGTAAAA
1 TAAATTATAAAAATAAGTAAAA
**
31568 TAAATTATAAATTTAAGTAAA
1 TAAATTATAAAAATAAGTAAA
31589 CAAGATGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (22 bp):
TAAATTATAAAAATAAGTAAAA
Found at i:32603 original size:6 final size:6
Alignment explanation
Indices: 32592--32620 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
32582 TATAGTCGGA
32592 GAAGGG GAAGGG GAAGGG GAAGGG GAAGG
1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGG
32621 AAAGAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:34981 original size:35 final size:37
Alignment explanation
Indices: 34915--34985 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 37
34905 ATTTTATAAG
34915 TTTTTCTATTTGTTGCAATTTTTAATATTTTATTTTA
1 TTTTTCTATTTGTTGCAATTTTTAATATTTTATTTTA
* *
34952 TTTTT-TATTT-TTGTAATTTTATCAT-TTTTATTTT
1 TTTTTCTATTTGTTGCAATTTT-TAATATTTTATTTT
34986 TCTATTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 18 0.58
36 8 0.26
37 5 0.16
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (37 bp):
TTTTTCTATTTGTTGCAATTTTTAATATTTTATTTTA
Found at i:35002 original size:23 final size:23
Alignment explanation
Indices: 34946--34994 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
34936 TTAATATTTT
*
34946 ATTTTAT--TTTTTATTTTTGTA
1 ATTTTATCATTTTTATTTTTCTA
34967 ATTTTATCATTTTTATTTTTCT-
1 ATTTTATCATTTTTATTTTTCTA
34989 ATTTTA
1 ATTTTA
34995 ATAGTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 7 0.28
22 6 0.24
23 12 0.48
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (23 bp):
ATTTTATCATTTTTATTTTTCTA
Found at i:35004 original size:9 final size:9
Alignment explanation
Indices: 34989--35022 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
34979 TTATTTTTCT
34989 ATTTTAATA
1 ATTTTAATA
*
34998 GTTTTAATA
1 ATTTTAATA
*
35007 ATTTTCATA
1 ATTTTAATA
35016 ATTTTAA
1 ATTTTAA
35023 GATGCTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (9 bp):
ATTTTAATA
Found at i:37226 original size:4 final size:4
Alignment explanation
Indices: 37217--37280 Score: 67
Period size: 4 Copynumber: 15.5 Consensus size: 4
37207 AAATAAACGG
* *
37217 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAAG GAGAG GAAA GAAA G-AA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA -GAAA GA-AA GAAA GAAA GAAA
*
37267 GAAT GAAA GAAA GA
1 GAAA GAAA GAAA GA
37281 TAATGTGATT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
3 3 0.06
4 38 0.73
5 11 0.21
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:37234 original size:13 final size:13
Alignment explanation
Indices: 37216--37279 Score: 71
Period size: 13 Copynumber: 5.1 Consensus size: 13
37206 CAAATAAACG
37216 GGAAAGAAAGAAA
1 GGAAAGAAAGAAA
37229 GGAAAGAAAGAAA
1 GGAAAGAAAGAAA
* *
37242 -GAAAGGAAGGAGA
1 GGAAA-GAAAGAAA
37255 GGAAAGAAAG-AA
1 GGAAAGAAAGAAA
*
37267 -GAATGAAAGAAA
1 GGAAAGAAAGAAA
37279 G
1 G
37280 ATAATGTGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
11 8 0.19
12 7 0.17
13 23 0.55
14 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (13 bp):
GGAAAGAAAGAAA
Found at i:37239 original size:17 final size:17
Alignment explanation
Indices: 37217--37279 Score: 76
Period size: 17 Copynumber: 3.8 Consensus size: 17
37207 AAATAAACGG
37217 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
*
37234 GAAAGAAAGAAAGGAAG
1 GAAAGAAAGAAAGGAAA
*
37251 GAGAGGAAAGAAA-G-AA
1 GA-AAGAAAGAAAGGAAA
*
37267 GAATGAAAGAAAG
1 GAAAGAAAGAAAG
37280 ATAATGTGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
15 9 0.22
16 3 0.08
17 19 0.47
18 9 0.22
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Done.