Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005335.1 Kokia drynarioides strain JFW-HI SEQ_119288, 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: 2135
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Found at i:228 original size:31 final size:31
Alignment explanation
Indices: 193--256 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
183 AAAATTCTCC
* *
193 AAAATTATATTTTTAACCCT-AAATTTTCAAA
1 AAAATTACATTTTT-ACCCTCAAACTTTCAAA
*
224 AAAATTACATTTTTACCCTCAAACTTTCTAA
1 AAAATTACATTTTTACCCTCAAACTTTCAAA
255 AA
1 AA
257 TTCCATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (31 bp):
AAAATTACATTTTTACCCTCAAACTTTCAAA
Found at i:258 original size:60 final size:60
Alignment explanation
Indices: 162--295 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 60
152 TAAACAATCC
* * * *
162 AAAAATTATATTTTGACCCTTAAAATTCTCCAAAATTATATTTTTAACCCTAAATTTTCAA
1 AAAAATTACATTTTGACCCTCAAAATTCTCCAAAATTACATTTTTAACCCCAAATTTTC-A
* * * * * * *
223 AAAAATTACATTTTTACCCTCAAACTT-TCTAAAATTCCATTTTTGACCCCAATTTTTCT
1 AAAAATTACATTTTGACCCTCAAAATTCTCCAAAATTACATTTTTAACCCCAAATTTTCA
282 AAAAATTACCATTT
1 AAAAATTA-CATTT
296 ACCTCCGAAC
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 8 0.13
60 30 0.49
61 23 0.38
ACGTcount: A:0.38, C:0.19, G:0.01, T:0.41
Consensus pattern (60 bp):
AAAAATTACATTTTGACCCTCAAAATTCTCCAAAATTACATTTTTAACCCCAAATTTTCA
Found at i:352 original size:30 final size:29
Alignment explanation
Indices: 306--471 Score: 92
Period size: 30 Copynumber: 5.7 Consensus size: 29
296 ACCTCCGAAC
*
306 TTCCAAAAAATTCCATTTTTTACCTCGATTT
1 TTCC-AAAAATACCATTTTTTACCTCGA-TT
* * **
337 TTCCAAAAATACCA--TTTTACCCCTAAAC
1 TTCCAAAAATACCATTTTTTACCTC-GATT
* * * *
365 TTCCCAAAATTCAATTTTTGACCAT-GATT
1 TTCCAAAAATACCATTTTTTACC-TCGATT
**
394 TTCCAAAAATTACCA--TTTTACCCTCGAAC
1 TTCCAAAAA-TACCATTTTTTA-CCTCGATT
* * *
423 TTCGAAAAATTCCATTTTTGACCTCGATTT
1 TTCCAAAAATACCATTTTTTACCTCGA-TT
453 TTCCAAAAATTA-CATTTTT
1 TTCCAAAAA-TACCATTTTT
472 ACCCCAAGCT
Statistics
Matches: 98, Mismatches: 26, Indels: 23
0.67 0.18 0.16
Matches are distributed among these distances:
28 28 0.29
29 28 0.29
30 37 0.38
31 5 0.05
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (29 bp):
TTCCAAAAATACCATTTTTTACCTCGATT
Found at i:485 original size:29 final size:29
Alignment explanation
Indices: 223--505 Score: 133
Period size: 29 Copynumber: 9.7 Consensus size: 29
213 AAATTTTCAA
*
223 AAAAATTACATTTTTACCCTCAAACTTT-C
1 AAAAATTACATTTTTACCC-CAATCTTTCC
* * * *
252 TAAAATTCCATTTTTGACCCCAATTTTTCT
1 AAAAATTACATTTTT-ACCCCAATCTTTCC
282 AAAAATTACCA--TTTACCTCCGAA-C-TTCC
1 AAAAATTA-CATTTTTACC-CC-AATCTTTCC
* * * *
310 AAAAAATTCCATTTTTTACCTCGATTTTTCC
1 -AAAAATTACA-TTTTTACCCCAATCTTTCC
*
341 AAAAA-TACCA-TTTTACCCCTAAAC-TTCC
1 AAAAATTA-CATTTTTACCCC-AATCTTTCC
* ***
369 CAAAATT-CAATTTTTGACCATGAT-TTTCC
1 AAAAATTAC-ATTTTT-ACCCCAATCTTTCC
*
398 AAAAATTACCA-TTTTACCCTCGAA-C-TTCG
1 AAAAATTA-CATTTTTACCC-C-AATCTTTCC
* * * *
427 AAAAATTCCATTTTTGACCTCGATTTTTCC
1 AAAAATTACATTTTT-ACCCCAATCTTTCC
*
457 AAAAATTACATTTTTACCCCAAGCTTTCC
1 AAAAATTACATTTTTACCCCAATCTTTCC
* * *
486 CAAAATTACTTTTTTTCCCC
1 AAAAATTACATTTTTACCCC
506 CTTGAGTGTC
Statistics
Matches: 186, Mismatches: 41, Indels: 54
0.66 0.15 0.19
Matches are distributed among these distances:
27 1 0.01
28 31 0.17
29 96 0.52
30 45 0.24
31 13 0.07
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (29 bp):
AAAAATTACATTTTTACCCCAATCTTTCC
Found at i:500 original size:59 final size:58
Alignment explanation
Indices: 223--476 Score: 295
Period size: 58 Copynumber: 4.3 Consensus size: 58
213 AAATTTTCAA
* * * * * *
223 AAAAATTA-CATTTTTACCCTCAAACTTTCTAAAATTCCATTTTTGACCCCAATTTTTCT
1 AAAAATTACCA-TTTTACCC-CGAACTTCCAAAAATTCCATTTTTGACCTCGATTTTTCC
*
282 AAAAATTACCA-TTTACCTCCGAACTTCCAAAAAATTCCATTTTTTACCTCGATTTTTCC
1 AAAAATTACCATTTTACC-CCGAACTTCC-AAAAATTCCATTTTTGACCTCGATTTTTCC
* * *
341 AAAAA-TACCATTTTACCCCTAAACTTCCCAAAATTCAATTTTTGACCAT-GA-TTTTCC
1 AAAAATTACCATTTTACCCC-GAACTTCCAAAAATTCCATTTTTGACC-TCGATTTTTCC
*
398 AAAAATTACCATTTTACCCTCGAACTTCGAAAAATTCCATTTTTGACCTCGATTTTTCC
1 AAAAATTACCATTTTACCC-CGAACTTCCAAAAATTCCATTTTTGACCTCGATTTTTCC
457 AAAAATTA-CATTTTTACCCC
1 AAAAATTACCA-TTTTACCCC
477 AAGCTTTCCC
Statistics
Matches: 169, Mismatches: 15, Indels: 23
0.82 0.07 0.11
Matches are distributed among these distances:
57 12 0.07
58 79 0.47
59 76 0.45
60 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.38
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCGAACTTCCAAAAATTCCATTTTTGACCTCGATTTTTCC
Found at i:550 original size:29 final size:29
Alignment explanation
Indices: 277--558 Score: 115
Period size: 29 Copynumber: 9.7 Consensus size: 29
267 GACCCCAATT
* *
277 TTTCTAAAAATTACCA-TTTA-CCTCCGAA
1 TTTCCAAAAATTACCATTTTACCCT-CGAG
* *
305 CTTCCAAAAAATT-CCATTTTTTA-CCTCGATT
1 TTTCC-AAAAATTACCA--TTTTACCCTCGA-G
* *
336 TTTCCAAAAA-TACCATTTTACCC-CTAAA
1 TTTCCAAAAATTACCATTTTACCCTC-GAG
* * * * *
364 CTTCCCAAAATT-CAATTTTTGACCAT-GAT
1 TTTCCAAAAATTACCA-TTTT-ACCCTCGAG
*
393 TTTCCAAAAATTACCATTTTACCCTCGAA
1 TTTCCAAAAATTACCATTTTACCCTCGAG
* * *
422 CTTCGAAAAATT-CCATTTTTGA-CCTCGATT
1 TTTCCAAAAATTACCA-TTTT-ACCCTCGA-G
*
452 TTTCCAAAAATTA-CATTTTTACCC-CAAG
1 TTTCCAAAAATTACCA-TTTTACCCTCGAG
* ** * *
480 CTTTCCCAAAATTACTTTTTTTCCCCCTTGAG
1 -TTTCCAAAAATTAC-CATTTT-ACCCTCGAG
* *
512 TGTCC-AAAATTACCATTTTACCCTCGGG
1 TTTCCAAAAATTACCATTTTACCCTCGAG
*
540 TTTCCAAAAATCA-CATTTT
1 TTTCCAAAAATTACCATTTT
559 CAAACCCCGA
Statistics
Matches: 191, Mismatches: 38, Indels: 50
0.68 0.14 0.18
Matches are distributed among these distances:
28 45 0.24
29 78 0.41
30 48 0.25
31 18 0.09
32 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (29 bp):
TTTCCAAAAATTACCATTTTACCCTCGAG
Done.