Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013575.1 Kokia drynarioides strain JFW-HI SEQ_128601, 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: 68295
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:3897 original size:5 final size:5
Alignment explanation
Indices: 3887--3917 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
3877 ATCGAAAATT
3887 GAATC GAATC GAATC GAATC GAATC GAATC G
1 GAATC GAATC GAATC GAATC GAATC GAATC G
3918 TAATAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (5 bp):
GAATC
Found at i:11534 original size:5 final size:5
Alignment explanation
Indices: 11524--11551 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
11514 CTCACCCCAT
11524 TTCTC TTCTC TTCTC TTCTC TTCTC TTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTC
11552 CCACTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TTCTC
Found at i:12861 original size:31 final size:29
Alignment explanation
Indices: 12792--12863 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 29
12782 TTCGATAAAT
*
12792 AAAAA-AATATAAAATTATTAAATATTAA
1 AAAAATAATATAAAATTATTAAAAATTAA
* *
12820 AATAATATAATATAAATATTTTTAAAAATTTTA
1 AA-AA-ATAATATAAA-ATTATTAAAAA-TTAA
12853 AAAAATAATAT
1 AAAAATAATAT
12864 GGGTGGGCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
28 2 0.06
29 2 0.06
30 1 0.03
31 15 0.42
32 11 0.31
33 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAAATAATATAAAATTATTAAAAATTAA
Found at i:13230 original size:31 final size:30
Alignment explanation
Indices: 13191--13263 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
13181 TAGGCCCGCG
13191 TATTTTTTA-TATATATATTTAAAAATATTA
1 TATTTTTTATTATA-ATATTTAAAAATATTA
* * *
13221 TATTGTTTTATTTTAATATTTAATAATTTTA
1 TATT-TTTTATTATAATATTTAAAAATATTA
*
13252 TACATTTTTATT
1 TA-TTTTTTATT
13264 TGTTGAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 4 0.11
31 28 0.78
32 4 0.11
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (30 bp):
TATTTTTTATTATAATATTTAAAAATATTA
Found at i:14459 original size:29 final size:30
Alignment explanation
Indices: 14425--14488 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
14415 AACACAAGTA
*
14425 ACTAAAACGTAACATT-T-CAAATATAAATG
1 ACTAAAACGTAAC-TTATACAAATAAAAATG
*
14454 ACTAAAATGTAACTTGATACAAATAAAAATG
1 ACTAAAACGTAACTT-ATACAAATAAAAATG
14485 ACTA
1 ACTA
14489 TTTTAACAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.07
29 12 0.40
30 1 0.03
31 15 0.50
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (30 bp):
ACTAAAACGTAACTTATACAAATAAAAATG
Found at i:15631 original size:29 final size:28
Alignment explanation
Indices: 15599--15661 Score: 65
Period size: 30 Copynumber: 2.2 Consensus size: 28
15589 TTAATTAAAA
15599 AAAATTATAATTT-AATCATTAAACTATTT
1 AAAATTATAATTTGAA-CATTAAACTA-TT
* * *
15628 AAAAGTTTTTATTTGAACATTAAGCTATT
1 AAAA-TTATAATTTGAACATTAAACTATT
15657 AAAAT
1 AAAAT
15662 CTATGCTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.03
29 10 0.34
30 16 0.55
31 2 0.07
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (28 bp):
AAAATTATAATTTGAACATTAAACTATT
Found at i:29041 original size:15 final size:17
Alignment explanation
Indices: 29008--29050 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
28998 GAAGGAAAAA
29008 AAAAAAACCA-ATATGAT
1 AAAAAAA-CATATATGAT
29025 -AAAAAACATATAT-AT
1 AAAAAAACATATATGAT
29040 AAAAAAACATA
1 AAAAAAACATA
29051 AAATACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.19
Consensus pattern (17 bp):
AAAAAAACATATATGAT
Found at i:29519 original size:33 final size:31
Alignment explanation
Indices: 29466--29534 Score: 111
Period size: 33 Copynumber: 2.2 Consensus size: 31
29456 TATTTACCAA
29466 ATTTATATATTATTACATATATCATATTCAT
1 ATTTATATATTATTACATATATCATATTCAT
*
29497 ATTTATATATATATATATATATATCATATTCAT
1 ATTTATATAT-TAT-TACATATATCATATTCAT
29530 ATTTA
1 ATTTA
29535 ATTTAATCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 10 0.29
32 3 0.09
33 22 0.63
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (31 bp):
ATTTATATATTATTACATATATCATATTCAT
Found at i:30344 original size:17 final size:18
Alignment explanation
Indices: 30311--30347 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
30301 TCATTTAAAA
30311 ATTAAAAAGATATAAATT
1 ATTAAAAAGATATAAATT
30329 ATTAAAATAG-TA-AAATT
1 ATTAAAA-AGATATAAATT
30346 AT
1 AT
30348 ATTTTTACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 9 0.50
19 2 0.11
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
ATTAAAAAGATATAAATT
Found at i:33394 original size:20 final size:21
Alignment explanation
Indices: 33361--33399 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
33351 ATTCAATTTG
*
33361 AAAATTTTTCGAATCGAGTCA
1 AAAAATTTTCGAATCGAGTCA
33382 AAAAATTTT-GAATCGAGT
1 AAAAATTTTCGAATCGAGT
33400 TGAGTCGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (21 bp):
AAAAATTTTCGAATCGAGTCA
Found at i:35358 original size:26 final size:28
Alignment explanation
Indices: 35306--35358 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
35296 ACTTTTATAA
* *
35306 GTACCAACTTGAACAAAAACAATATTAG
1 GTACCAAATTGAACAAAAACAAAATTAG
*
35334 GTACCAAATT-AAGAAAAA-AAAATTA
1 GTACCAAATTGAACAAAAACAAAATTA
35359 AATTCAGGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 6 0.27
27 7 0.32
28 9 0.41
ACGTcount: A:0.57, C:0.13, G:0.09, T:0.21
Consensus pattern (28 bp):
GTACCAAATTGAACAAAAACAAAATTAG
Found at i:35465 original size:31 final size:31
Alignment explanation
Indices: 35386--35466 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
35376 GAATCCCAAA
* *
35386 AAATTTAAGTACCAATTTAAGAAAAAATGTC
1 AAATTTAAGTATCAAATTAAGAAAAAATGTC
* * *
35417 AAGTTTATGTATTAAATTAA-AAAAAGATGTC
1 AAATTTAAGTATCAAATTAAGAAAAA-ATGTC
*
35448 AAATTTAAATATCAAATTA
1 AAATTTAAGTATCAAATTA
35467 TATTAAAAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 5 0.12
31 35 0.88
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (31 bp):
AAATTTAAGTATCAAATTAAGAAAAAATGTC
Found at i:35508 original size:55 final size:58
Alignment explanation
Indices: 35443--35552 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 58
35433 TTAAAAAAAG
*
35443 ATGTCAAATTTAAATATC-AA-ATTATATTAA-AAATTTTAAATACTAAAATAATAAA
1 ATGTCAAATTTAAATATCAAATATTATATTAAGAAATTTTAAATAATAAAATAATAAA
* * * *
35498 ATGTTAAATTTAATTATCAAATATTATATTAAGTCAATTTTAAATAATGAAATAA
1 ATGTCAAATTTAAATATCAAATATTATATTAAG-AAATTTTAAATAATAAAATAA
35553 AATAACCTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
55 16 0.35
56 2 0.04
57 10 0.22
59 18 0.39
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.39
Consensus pattern (58 bp):
ATGTCAAATTTAAATATCAAATATTATATTAAGAAATTTTAAATAATAAAATAATAAA
Found at i:41462 original size:19 final size:19
Alignment explanation
Indices: 41435--41502 Score: 50
Period size: 19 Copynumber: 3.5 Consensus size: 19
41425 AGTTTGATGT
*
41435 AAATTTGTTTGTGATCTAA
1 AAATATGTTTGTGATCTAA
*
41454 AAATATGTTAACTTGTGATGT--
1 AAATATG-T---TTGTGATCTAA
* *
41475 AAATTTGTTTGTGATTTAA
1 AAATATGTTTGTGATCTAA
41494 AAATATGTT
1 AAATATGTT
41503 AACTTCCTAC
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
17 8 0.21
19 14 0.37
20 2 0.05
21 6 0.16
23 8 0.21
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (19 bp):
AAATATGTTTGTGATCTAA
Found at i:41477 original size:23 final size:23
Alignment explanation
Indices: 41443--41507 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 23
41433 GTAAATTTGT
41443 TTGTGATCTAAAAATATGTTAAC
1 TTGTGATCTAAAAATATGTTAAC
* *
41466 TTGTGATGT--AAATTTG-T---
1 TTGTGATCTAAAAATATGTTAAC
*
41483 TTGTGATTTAAAAATATGTTAAC
1 TTGTGATCTAAAAATATGTTAAC
41506 TT
1 TT
41508 CCTACTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
17 8 0.25
19 6 0.19
20 2 0.06
21 6 0.19
23 10 0.31
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (23 bp):
TTGTGATCTAAAAATATGTTAAC
Found at i:41484 original size:40 final size:40
Alignment explanation
Indices: 41429--41507 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
41419 ATGCCTAGTT
41429 TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTTG
1 TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTTG
*
41469 TGATGTAAATTTGTTTGTGATTTAAAAATATGTTAACTT
1 TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTT
41508 CCTACTTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (40 bp):
TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTTG
Found at i:41488 original size:17 final size:17
Alignment explanation
Indices: 41429--41494 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 17
41419 ATGCCTAGTT
41429 TGATGTAAATTTGTTTG
1 TGATGTAAATTTGTTTG
* *
41446 TGATCTAAAAATATGTTAACTTG
1 TGATGT--AAATTTG-T---TTG
41469 TGATGTAAATTTGTTTG
1 TGATGTAAATTTGTTTG
*
41486 TGATTTAAA
1 TGATGTAAA
41495 AATATGTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
17 16 0.42
19 6 0.16
20 2 0.05
21 6 0.16
23 8 0.21
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (17 bp):
TGATGTAAATTTGTTTG
Found at i:43409 original size:33 final size:33
Alignment explanation
Indices: 43367--43451 Score: 134
Period size: 33 Copynumber: 2.6 Consensus size: 33
43357 TTTAAAGGAG
* *
43367 ATAGCCTCCGTTCAGACAGCAGTAAGCAAAGTA
1 ATAGTCTCCGCTCAGACAGCAGTAAGCAAAGTA
**
43400 ATAGTCTCCGCTCAGATGGCAGTAAGCAAAGTA
1 ATAGTCTCCGCTCAGACAGCAGTAAGCAAAGTA
43433 ATAGTCTCCGCTCAGACAG
1 ATAGTCTCCGCTCAGACAG
43452 TGCAAAACGT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (33 bp):
ATAGTCTCCGCTCAGACAGCAGTAAGCAAAGTA
Found at i:55045 original size:14 final size:15
Alignment explanation
Indices: 55006--55048 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
54996 TTTTTGTACA
55006 TTTT-AAAATTTAGT
1 TTTTAAAAATTTAGT
* *
55020 TTTTATACATTTA-T
1 TTTTAAAAATTTAGT
55034 TTTTAAAAATTTAGT
1 TTTTAAAAATTTAGT
55049 CCTTCCACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (15 bp):
TTTTAAAAATTTAGT
Found at i:59886 original size:18 final size:18
Alignment explanation
Indices: 59863--59906 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
59853 TTATACGACC
* *
59863 AAAATAAATGAAATATCT
1 AAAATAAATGAAAAATAT
*
59881 AAAATATATGAAAAATAT
1 AAAATAAATGAAAAATAT
59899 -AAATAAAT
1 AAAATAAAT
59907 TATACAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (18 bp):
AAAATAAATGAAAAATAT
Found at i:64396 original size:18 final size:18
Alignment explanation
Indices: 64361--64397 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
64351 GTTATACTTA
64361 AAGAACAACTTATCTAGT
1 AAGAACAACTTATCTAGT
64379 AAGAACAACTTATCTAGT
1 AAGAACAACTTATCTAGT
64397 A
1 A
64398 TTGTTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (18 bp):
AAGAACAACTTATCTAGT
Found at i:67527 original size:84 final size:84
Alignment explanation
Indices: 67378--67544 Score: 273
Period size: 84 Copynumber: 2.0 Consensus size: 84
67368 TATCATCAAA
* * *
67378 AATCATTCTATTATCAATGAATAAAAATAGAGTATAAAAAATTCATTTATTATATGTCGAGATTT
1 AATCATTCTATTATCAATGAATAAAAATAGAGTATAAAAAATTCATCTATTATATATCGAAATTT
*
67443 TAGTTTAATCAATGTGTGG
66 TAGTTTAATCAACGTGTGG
*
67462 AATCATTCTATTATCAATGAATAAAAATGGAGTATAAAAAATTCATCTATTATGA-ATCGAAATT
1 AATCATTCTATTATCAATGAATAAAAATAGAGTATAAAAAATTCATCTATTAT-ATATCGAAATT
67526 TTAGTTTAATCAACGTGTG
65 TTAGTTTAATCAACGTGTG
67545 ATTTAAGTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
84 76 0.99
85 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (84 bp):
AATCATTCTATTATCAATGAATAAAAATAGAGTATAAAAAATTCATCTATTATATATCGAAATTT
TAGTTTAATCAACGTGTGG
Done.