Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001173.1 Kokia drynarioides strain JFW-HI SEQ_112502, 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: 24450
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Found at i:1880 original size:33 final size:33
Alignment explanation
Indices: 1841--1908 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
1831 TTTCTTTAAA
1841 AATGAGTTTAGTCAAATTATCTTGGATCTCTCT
1 AATGAGTTTAGTCAAATTATCTTGGATCTCTCT
1874 AATGAGTTTAGTCAAATTATCTTGGATCTCTCT
1 AATGAGTTTAGTCAAATTATCTTGGATCTCTCT
1907 AA
1 AA
1909 GGCCCATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (33 bp):
AATGAGTTTAGTCAAATTATCTTGGATCTCTCT
Found at i:5344 original size:22 final size:22
Alignment explanation
Indices: 5319--5364 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5309 AAGGGTCAAA
5319 ATGCTTATGTGAAACATGTAAC
1 ATGCTTATGTGAAACATGTAAC
5341 ATGCTTATGTGAAACATGTAAC
1 ATGCTTATGTGAAACATGTAAC
5363 AT
1 AT
5365 AGTCATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (22 bp):
ATGCTTATGTGAAACATGTAAC
Found at i:9497 original size:21 final size:21
Alignment explanation
Indices: 9473--9526 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
9463 TGGGAGGGTT
9473 CTACCGATACAAGTATAACTA
1 CTACCGATACAAGTATAACTA
* * * *
9494 CTACCGATATAATTATTACTT
1 CTACCGATACAAGTATAACTA
*
9515 CTATCGATACAA
1 CTACCGATACAA
9527 CAAACTCTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.31
Consensus pattern (21 bp):
CTACCGATACAAGTATAACTA
Found at i:9988 original size:21 final size:21
Alignment explanation
Indices: 9964--10015 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
9954 AGATTCCTAT
9964 CGATACAAGTGACAATTCTAC
1 CGATACAAGTGACAATTCTAC
**
9985 CGATACAAGTGACTTTTCTAC
1 CGATACAAGTGACAATTCTAC
* *
10006 CTAAACAAGT
1 CGATACAAGT
10016 TTTACTTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (21 bp):
CGATACAAGTGACAATTCTAC
Found at i:10779 original size:38 final size:37
Alignment explanation
Indices: 10707--10784 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 37
10697 GTGATCCAAT
* * * *
10707 ATTGCTCTTATGAGCTAGTATTGCTCAACAAGCCAGA
1 ATTGCTCTTACGAGCCAATATTACTCAACAAGCCAGA
*
10744 ATTGCTCTTACGAGCCAATATTTACTCAACGAGCCAGA
1 ATTGCTCTTACGAGCCAATA-TTACTCAACAAGCCAGA
10782 ATT
1 ATT
10785 TCTCAGTGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
37 17 0.49
38 18 0.51
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (37 bp):
ATTGCTCTTACGAGCCAATATTACTCAACAAGCCAGA
Found at i:10785 original size:19 final size:18
Alignment explanation
Indices: 10730--10789 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
10720 GCTAGTATTG
* *
10730 CTCAACAAGCCAGAATTG
1 CTCAACGAGCCAGAATTT
*
10748 CTCTTACGAGCCA-ATATTT
1 CTC-AACGAGCCAGA-ATTT
10767 ACTCAACGAGCCAGAATTT
1 -CTCAACGAGCCAGAATTT
10786 CTCA
1 CTCA
10790 GTGAGTCAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 8 0.24
19 22 0.65
20 4 0.12
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.25
Consensus pattern (18 bp):
CTCAACGAGCCAGAATTT
Found at i:12682 original size:94 final size:94
Alignment explanation
Indices: 12518--12740 Score: 308
Period size: 94 Copynumber: 2.4 Consensus size: 94
12508 AAATTGTCTC
* * **
12518 TGTTACCAGTATACGATGCTGCTCACTCTAAGCTGACGAGTACTTGCAACATATGCGGTACCTCA
1 TGTTACCAGTATACGATGCTGCTCACACTAAGCTGACGAGGACTCACAACATATGCGGTACCTCA
12583 ACCATTGATACGGTATATGTACATATAAT
66 ACCATTGATACGGTATATGTACATATAAT
* *
12612 TGTTACCAGTATATGATGCTGCTCACACTAAGCTGACGAGGACTCACAACATATGTGGTACCTCA
1 TGTTACCAGTATACGATGCTGCTCACACTAAGCTGACGAGGACTCACAACATATGCGGTACCTCA
* * *
12677 GCCATTGATACGGTATCTGTACATATAAC
66 ACCATTGATACGGTATATGTACATATAAT
* * * *
12706 TATT-CC-CTA-ACGATGTTGCTCACACTAAGTTGACG
1 TGTTACCAGTATACGATGCTGCTCACACTAAGCTGACG
12741 GGAATATGCA
Statistics
Matches: 115, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
91 23 0.20
92 2 0.02
93 2 0.02
94 88 0.77
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (94 bp):
TGTTACCAGTATACGATGCTGCTCACACTAAGCTGACGAGGACTCACAACATATGCGGTACCTCA
ACCATTGATACGGTATATGTACATATAAT
Found at i:13364 original size:16 final size:16
Alignment explanation
Indices: 13340--13371 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
13330 TCCTTACAAA
*
13340 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
13356 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
13372 AAAATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:20018 original size:41 final size:41
Alignment explanation
Indices: 19958--20053 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
19948 TTGTTTGTAG
* *
19958 AGAATTCTTGTCAATGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
19999 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
*
20040 AAAATTCTTGTTAA
1 AGAATTCTTGTTAA
20054 AATAAAATTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.38
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
Done.