Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007075.1 Kokia drynarioides strain JFW-HI SEQ_121684, 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: 60539
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 56 characters in sequence are not A, C, G, or T
Found at i:14208 original size:16 final size:16
Alignment explanation
Indices: 14178--14225 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
14168 AATGATTTCA
14178 ATAAATAA-AAAATAT
1 ATAAATAATAAAATAT
*
14193 ATAAATAATTAAATAT
1 ATAAATAATAAAATAT
*
14209 -TAAAATAATACAATAT
1 AT-AAATAATAAAATAT
14225 A
1 A
14226 ATTTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAATAATAAAATAT
Found at i:22215 original size:16 final size:16
Alignment explanation
Indices: 22194--22242 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
22184 ATGGGACGAG
22194 AATAAATTTTAAATTA
1 AATAAATTTTAAATTA
22210 AATAAA-TTT-AATTA
1 AATAAATTTTAAATTA
*
22224 ATTGAAAATTTTAAATTA
1 AAT--AAATTTTAAATTA
22242 A
1 A
22243 TTGCACCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 7 0.25
15 3 0.11
16 9 0.32
17 3 0.11
18 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
AATAAATTTTAAATTA
Found at i:22240 original size:18 final size:17
Alignment explanation
Indices: 22197--22245 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
22187 GGACGAGAAT
*
22197 AAATTTTAAATTAAAT-
1 AAATTTTAAATTAATTG
22213 AAA-TTT-AATTAATTG
1 AAATTTTAAATTAATTG
22228 AAAATTTTAAATTAATTG
1 -AAATTTTAAATTAATTG
22246 CACCTTGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 7 0.25
15 3 0.11
16 6 0.21
17 3 0.11
18 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (17 bp):
AAATTTTAAATTAATTG
Found at i:23377 original size:25 final size:24
Alignment explanation
Indices: 23295--23383 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 24
23285 ATTATGAAAT
23295 TAAAATATATAAAATATCATATTTTA-C
1 TAAAA-ATATAAAA-AT-AT-TTTTATC
* *
23322 -AAAAATAT-AAAATATATTTGTC
1 TAAAAATATAAAAATATTTTTATC
*
23344 TAAACATATAAAAATATGTTTTATC
1 TAAAAATATAAAAATAT-TTTTATC
23369 TAAAAATATATAAAA
1 TAAAAATATA-AAAA
23384 CGCATAACTC
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
21 3 0.06
22 3 0.06
23 9 0.18
24 10 0.20
25 18 0.35
26 8 0.16
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (24 bp):
TAAAAATATAAAAATATTTTTATC
Found at i:24320 original size:4 final size:4
Alignment explanation
Indices: 24311--24336 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
24301 CTTACAAATG
24311 CAAA CAAA CAAA CAAA CAAA CAAA CA
1 CAAA CAAA CAAA CAAA CAAA CAAA CA
24337 TGCTATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.27, G:0.00, T:0.00
Consensus pattern (4 bp):
CAAA
Found at i:28298 original size:22 final size:22
Alignment explanation
Indices: 28273--28345 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
28263 TCGCAACACC
28273 AGATTCACGTTGTGGCAGGTAA
1 AGATTCACGTTGTGGCAGGTAA
* * ** *
28295 AGATGCACTGTTGGATCGCA-ACACC
1 AGATTCAC-GTT-G-TGGCAGGTA-A
28320 AGATTCACGTTGTGGCAGGTAA
1 AGATTCACGTTGTGGCAGGTAA
28342 AGAT
1 AGAT
28346 GAAAGCAGTT
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
22 15 0.42
23 5 0.14
24 5 0.14
25 11 0.31
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.25
Consensus pattern (22 bp):
AGATTCACGTTGTGGCAGGTAA
Found at i:28322 original size:47 final size:47
Alignment explanation
Indices: 28253--28346 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
28243 TATGATATTC
28253 CACTGTTGGATCGCAACACCAGATTCACGTTGTGGCAGGTAAAGATG
1 CACTGTTGGATCGCAACACCAGATTCACGTTGTGGCAGGTAAAGATG
28300 CACTGTTGGATCGCAACACCAGATTCACGTTGTGGCAGGTAAAGATG
1 CACTGTTGGATCGCAACACCAGATTCACGTTGTGGCAGGTAAAGATG
28347 AAAGCAGTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (47 bp):
CACTGTTGGATCGCAACACCAGATTCACGTTGTGGCAGGTAAAGATG
Found at i:44351 original size:21 final size:19
Alignment explanation
Indices: 44308--44361 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
44298 CACCAAATGT
*
44308 TTTTAAATTATTGTTTTAA
1 TTTTAAATTATTTTTTTAA
44327 TTTTAAATTATTTTTTGTAAA
1 TTTTAAATTATTTTTT-T-AA
*
44348 TTTTAAAATATTTT
1 TTTTAAATTATTTT
44362 AATTGAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 15 0.48
20 1 0.03
21 15 0.48
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTTAAATTATTTTTTTAA
Found at i:46402 original size:29 final size:29
Alignment explanation
Indices: 46358--46426 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
46348 ATTCGACAGT
46358 CACAAAGGCTCACATATAATAGATTCTA-C
1 CACAAAGGCTCACATATAATAGATTC-AGC
*
46387 CTCAAAGGCTCACATATAATAGATTCAGC
1 CACAAAGGCTCACATATAATAGATTCAGC
46416 CACAAAGGCTC
1 CACAAAGGCTC
46427 TTCACTTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 1 0.03
29 36 0.97
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.22
Consensus pattern (29 bp):
CACAAAGGCTCACATATAATAGATTCAGC
Found at i:50072 original size:83 final size:83
Alignment explanation
Indices: 49933--50098 Score: 314
Period size: 83 Copynumber: 2.0 Consensus size: 83
49923 AAAATTCGAG
*
49933 AAGGAATTTGGATAAATAATTAAGCATATTTAAAATAAAGGAGGGATTGTATGAAATTGTGATTC
1 AAGGAATTTGGATAAATAATTAAGCATATTTAAAATAAAGGAGGGATTGTATGAAATTATGATTC
49998 TACGTCATTCATATCCCA
66 TACGTCATTCATATCCCA
*
50016 AAGGAATTTGGATAAATAATTAAGCATATTTAAAATAGAGGAGGGATTGTATGAAATTATGATTC
1 AAGGAATTTGGATAAATAATTAAGCATATTTAAAATAAAGGAGGGATTGTATGAAATTATGATTC
50081 TACGTCATTCATATCCCA
66 TACGTCATTCATATCCCA
50099 TTTCGATAGG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.33
Consensus pattern (83 bp):
AAGGAATTTGGATAAATAATTAAGCATATTTAAAATAAAGGAGGGATTGTATGAAATTATGATTC
TACGTCATTCATATCCCA
Done.