Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014787.1 Kokia drynarioides strain JFW-HI SEQ_129829, 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: 19998
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Found at i:4758 original size:64 final size:64
Alignment explanation
Indices: 4657--4785 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
4647 TTGTCATCAT
4657 GCATCCAAATAATTCTATTTTCCCGTTCATTGCAATACTCCCATACACTTCACCATGTCCAAAA
1 GCATCCAAATAATTCTATTTTCCCGTTCATTGCAATACTCCCATACACTTCACCATGTCCAAAA
4721 GCATCCAAATAATTCTATTTTCCCGTTCATTGCAATACTCCCATACACTTCACCATGTCCAAAA
1 GCATCCAAATAATTCTATTTTCCCGTTCATTGCAATACTCCCATACACTTCACCATGTCCAAAA
4785 G
1 G
4786 TTTACTAAGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (64 bp):
GCATCCAAATAATTCTATTTTCCCGTTCATTGCAATACTCCCATACACTTCACCATGTCCAAAA
Found at i:6969 original size:18 final size:19
Alignment explanation
Indices: 6920--6969 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
6910 AAATATTTTT
*
6920 TTTTTTGTATTTTTAATAA
1 TTTTTTATATTTTTAATAA
* *
6939 TTTTATACT-TTTTTGA-AA
1 TTTTTTA-TATTTTTAATAA
6957 TTTTTTATATTTT
1 TTTTTTATATTTT
6970 AAAAAATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
17 1 0.04
18 12 0.48
19 11 0.44
20 1 0.04
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (19 bp):
TTTTTTATATTTTTAATAA
Found at i:7175 original size:21 final size:21
Alignment explanation
Indices: 7151--7226 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
7141 ATACTAGTAA
7151 CCTAAACTCTAAACCTAAGAC
1 CCTAAACTCTAAACCTAAGAC
* *
7172 CCT-AACTCTTAAATTCT-ATAC
1 CCTAAACTC-TAAA-CCTAAGAC
* * *
7193 CCTAAACTTTAAACCCAAGAT
1 CCTAAACTCTAAACCTAAGAC
*
7214 CATAAAC-CTAAAC
1 CCTAAACTCTAAAC
7227 TCAATATCCT
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
20 11 0.26
21 25 0.60
22 6 0.14
ACGTcount: A:0.42, C:0.30, G:0.03, T:0.25
Consensus pattern (21 bp):
CCTAAACTCTAAACCTAAGAC
Found at i:12261 original size:30 final size:30
Alignment explanation
Indices: 12227--12321 Score: 100
Period size: 30 Copynumber: 3.2 Consensus size: 30
12217 AAACTATCCA
* *
12227 AAAATTCTATTTTTGACCCCGAAACTTTTG
1 AAAATTCTATTTTTGACCCCAAAACTTTAG
* * * * *
12257 AAAATTATATTTTTTACCCCCAAACTTCAA
1 AAAATTCTATTTTTGACCCCAAAACTTTAG
* * *
12287 AAAATTCCATTCTTGACCCCAAAACTTTCG
1 AAAATTCTATTTTTGACCCCAAAACTTTAG
12317 AAAAT
1 AAAAT
12322 CACCATTTTG
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (30 bp):
AAAATTCTATTTTTGACCCCAAAACTTTAG
Found at i:12365 original size:59 final size:59
Alignment explanation
Indices: 12221--12419 Score: 215
Period size: 59 Copynumber: 3.4 Consensus size: 59
12211 GTCTCTAAAC
* * * * *
12221 TATCCAAAAATTCTATTTTTGACCCCGAAACTTTTGAAAATTA-TATTTTTTACCCCCAAA
1 TATCCAAAAATTCCATTTTTGACCCCAAAACTTTCGAAAATTACCA--TTTTACCCCCGAA
* * * *
12281 CT-TCAAAAAATTCCATTCTTGACCCCAAAACTTTCGAAAATCACCATTTTGCCCCCGAA
1 -TATCCAAAAATTCCATTTTTGACCCCAAAACTTTCGAAAATTACCATTTTACCCCCGAA
* * * *
12340 TATCCAAAAATTCCATTTTTAACCCCAAAACTTTC-AAAATTACCCTTTTACGCTCGAA
1 TATCCAAAAATTCCATTTTTGACCCCAAAACTTTCGAAAATTACCATTTTACCCCCGAA
* *
12398 TGTCCAAAAATTCCGTTTTTGA
1 TATCCAAAAATTCCATTTTTGA
12420 TCCCGTTTTT
Statistics
Matches: 116, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
58 38 0.33
59 41 0.35
60 35 0.30
61 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (59 bp):
TATCCAAAAATTCCATTTTTGACCCCAAAACTTTCGAAAATTACCATTTTACCCCCGAA
Found at i:12750 original size:12 final size:12
Alignment explanation
Indices: 12733--12765 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
12723 ACTCGCATGT
12733 TTGTTTTCAAAA
1 TTGTTTTCAAAA
12745 TTGTTTTCAAAA
1 TTGTTTTCAAAA
12757 TTGTTTTCA
1 TTGTTTTCA
12766 TAAAAACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (12 bp):
TTGTTTTCAAAA
Found at i:13818 original size:17 final size:17
Alignment explanation
Indices: 13742--13837 Score: 86
Period size: 17 Copynumber: 5.6 Consensus size: 17
13732 TCCAATTTTT
*
13742 AATTTTAATTTACTTTA
1 AATTTAAATTTACTTTA
* * *
13759 AGTTTGAATTT-GTTCTA
1 AATTTAAATTTACTT-TA
* * *
13776 AATTTAAATTCATTTTTG
1 AATTTAAATTTA-CTTTA
*
13794 AGTTTAAATTTACTTTA
1 AATTTAAATTTACTTTA
*
13811 AATTTAAATTTACTATA
1 AATTTAAATTTACTTTA
13828 AATTTAAATT
1 AATTTAAATT
13838 AACTAAAAAG
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
16 2 0.03
17 47 0.76
18 11 0.18
19 2 0.03
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTACTTTA
Found at i:13842 original size:17 final size:17
Alignment explanation
Indices: 13796--13842 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
13786 CATTTTTGAG
*
13796 TTTAAATTTACTTTAAA
1 TTTAAATTTACTATAAA
13813 TTTAAATTTACTATAAA
1 TTTAAATTTACTATAAA
*
13830 TTTAAATTAACTA
1 TTTAAATTTACTA
13843 AAAAGTCCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAAATTTACTATAAA
Found at i:14607 original size:15 final size:16
Alignment explanation
Indices: 14582--14615 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
14572 AGTTACAACC
14582 TAATAAATATTATTAA
1 TAATAAATATTATTAA
14598 TAAT-AATATTATTAA
1 TAATAAATATTATTAA
14613 TAA
1 TAA
14616 CAGTAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATAAATATTATTAA
Done.