Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012298.1 Kokia drynarioides strain JFW-HI SEQ_127299, 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: 6440
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3385 original size:17 final size:17
Alignment explanation
Indices: 3357--3429 Score: 103
Period size: 17 Copynumber: 4.4 Consensus size: 17
3347 TTAGAAATTG
3357 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
3373 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
3390 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
3407 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
3424 AATTTA
1 AATTTA
3430 AAAAGTCCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
16 5 0.10
17 45 0.90
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:3405 original size:7 final size:6
Alignment explanation
Indices: 3362--3431 Score: 60
Period size: 6 Copynumber: 12.2 Consensus size: 6
3352 AATTGAATTT
* *
3362 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTTGAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA
*
3408 ATTT-- ATTATAA AATTAA ATTTAA A
1 ATTTAA ATT-TAA ATTTAA ATTTAA A
3432 AAGTCCAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
4 7 0.13
5 5 0.10
6 34 0.65
7 6 0.12
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:4751 original size:23 final size:23
Alignment explanation
Indices: 4674--4751 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 23
4664 CGGTGACGCA
* *
4674 CGATGGCCGCGCGTCGGGATCGG
1 CGATGGCCACGCGACGGGATCGG
* *
4697 CGATGNCACACGCCGGACGGCGA-CGCA
1 CGATGGC-CACG-C-GACGG-GATCG-G
*
4724 CGATGGCCACGCGCCGGGATCGG
1 CGATGGCCACGCGACGGGATCGG
4747 CGATG
1 CGATG
4752 CGCGTGCGAC
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
23 13 0.31
24 9 0.21
25 2 0.05
26 10 0.24
27 8 0.19
ACGTcount: A:0.15, C:0.33, G:0.41, T:0.09
Consensus pattern (23 bp):
CGATGGCCACGCGACGGGATCGG
Found at i:4996 original size:30 final size:29
Alignment explanation
Indices: 4967--5423 Score: 258
Period size: 29 Copynumber: 15.8 Consensus size: 29
4957 GTCCTAAACT
*
4967 TTCTAAAAATTACCATTTTACCCCGAAAC
1 TTCTAAAAATTACCATTTTACCCCGAACC
* *
4996 TTCCAAAAA-TCCCATTTTTTACCCCGAACC
1 TTCTAAAAATTACCA--TTTTACCCCGAACC
* *
5026 TTCTAAAAATTACCATTTTACCCCCAAAC
1 TTCTAAAAATTACCATTTTACCCCGAACC
* *
5055 TTCCAAAAA-TCCCATTTTTAGCCCCGAACC
1 TTCTAAAAATTACCA-TTTTA-CCCCGAACC
5085 TTCTAAAAATTACCATTTTACCCCCGAA-C
1 TTCTAAAAATTACCATTTTA-CCCCGAACC
* * *
5114 TTCCAAAAA-TCCCATTTTTGA-CCCTAACC
1 TTCTAAAAATTACCA-TTTT-ACCCCGAACC
*
5143 TTCTAAAAATTACCA-TTTACCCATGAA-C
1 TTCTAAAAATTACCATTTTACCC-CGAACC
* * **
5171 TTCCAAAAA-TCCCATTTTTAGCCCTAAACC
1 TTCTAAAAATTACCA-TTTTA-CCCCGAACC
* *
5201 TTCTAAAAATAACCATTTGTGACCTCGAACC
1 TTCTAAAAATTACCATTT-T-ACCCCGAACC
*
5232 TTCTAAAAATTACC-----A---CTAA-C
1 TTCTAAAAATTACCATTTTACCCCGAACC
** **
5252 TTCTAAAAATCCCATTTTTTGACCCC-AAGCC
1 TTCTAAAAATTAC-CATTTT-ACCCCGAA-CC
5283 TTCTAAAAATTACCATTTTACCACCGAA-C
1 TTCTAAAAATTACCATTTTACC-CCGAACC
* * ***
5312 TTCCAAAAA-TCCCATTTTTAACCTTTAACC
1 TTCTAAAAATTACCA-TTTT-ACCCCGAACC
*
5342 TTCTAAAAATTACCATTTTACCCCCG-AGC
1 TTCTAAAAATTACCATTTTA-CCCCGAACC
* * *
5371 TTCCAAAAA-TCCCAATTTTGACTCCGAACC
1 TTCTAAAAATTACC-ATTTT-ACCCCGAACC
* * *
5401 CTC-CAAAATTACCATTTTGCCCC
1 TTCTAAAAATTACCATTTTACCCC
5424 CGTGCATTCG
Statistics
Matches: 327, Mismatches: 59, Indels: 85
0.69 0.13 0.18
Matches are distributed among these distances:
20 12 0.04
21 3 0.01
24 1 0.00
27 6 0.02
28 41 0.13
29 113 0.35
30 101 0.31
31 49 0.15
32 1 0.00
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (29 bp):
TTCTAAAAATTACCATTTTACCCCGAACC
Found at i:5059 original size:59 final size:59
Alignment explanation
Indices: 4967--5218 Score: 384
Period size: 59 Copynumber: 4.3 Consensus size: 59
4957 GTCCTAAACT
*
4967 TTCTAAAAATTACCATTTTACCCCGAAACTTCCAAAAATCCCATTTTTTA-CCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCA-TTTTTAGCCCCGAACC
5026 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAGCCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAGCCCCGAACC
* * *
5085 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTT-GACCCTAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAGCCCCGAACC
*** **
5143 TTCTAAAAATTACCA-TTTACCCATGAACTTCCAAAAATCCCATTTTTAGCCCTAAACC
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAGCCCCGAACC
*
5201 TTCTAAAAATAACCATTT
1 TTCTAAAAATTACCATTT
5219 GTGACCTCGA
Statistics
Matches: 180, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
57 30 0.17
58 50 0.28
59 100 0.56
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (59 bp):
TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAGCCCCGAACC
Found at i:5285 original size:51 final size:51
Alignment explanation
Indices: 5200--5297 Score: 137
Period size: 51 Copynumber: 1.9 Consensus size: 51
5190 AGCCCTAAAC
*
5200 CTTCTAAAAATAACCATTTGTGACCTCGAACCTTCTAAAAATTACCACTAA
1 CTTCTAAAAATAACCATTTGTGACCTCCAACCTTCTAAAAATTACCACTAA
* *
5251 CTTCTAAAAAT-CCCATTTTTTGACC-CCAAGCCTTCTAAAAATTACCA
1 CTTCTAAAAATAACCA-TTTGTGACCTCCAA-CCTTCTAAAAATTACCA
5298 TTTTACCACC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
50 6 0.14
51 36 0.86
ACGTcount: A:0.37, C:0.28, G:0.05, T:0.31
Consensus pattern (51 bp):
CTTCTAAAAATAACCATTTGTGACCTCCAACCTTCTAAAAATTACCACTAA
Found at i:5346 original size:59 final size:59
Alignment explanation
Indices: 5241--5389 Score: 194
Period size: 59 Copynumber: 2.5 Consensus size: 59
5231 CTTCTAAAAA
* * *
5241 TTACCA-CTAACTTCTAAAAATCCCATTTTTTGACCCCAAGCCTTCTAAAAATTACCATT
1 TTACCACCGAACTTCCAAAAATCCCA-TTTTTAACCCCAAGCCTTCTAAAAATTACCATT
**
5300 TTACCACCGAACTTCCAAAAATCCCATTTTTAACCTTTAA-CCTTCTAAAAATTACCATT
1 TTACCACCGAACTTCCAAAAATCCCATTTTTAACC-CCAAGCCTTCTAAAAATTACCATT
* * *
5359 TTACCCCCGAGCTTCCAAAAATCCCAATTTT
1 TTACCACCGAACTTCCAAAAATCCCATTTTT
5390 GACTCCGAAC
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
59 61 0.76
60 19 0.24
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (59 bp):
TTACCACCGAACTTCCAAAAATCCCATTTTTAACCCCAAGCCTTCTAAAAATTACCATT
Done.