Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002680.1 Kokia drynarioides strain JFW-HI SEQ_114945, 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: 15119
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:58 original size:27 final size:27
Alignment explanation
Indices: 28--82 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
18 ACACCCCTTA
28 GTGCCGCCACTT-GATATTCCTCCATTG
1 GTGCCGCCACTTCG-TATTCCTCCATTG
*
55 GTGCCGCCACTTCGTGTTCCTCCATTG
1 GTGCCGCCACTTCGTATTCCTCCATTG
82 G
1 G
83 GTATCAGGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.11, C:0.35, G:0.22, T:0.33
Consensus pattern (27 bp):
GTGCCGCCACTTCGTATTCCTCCATTG
Found at i:1108 original size:31 final size:32
Alignment explanation
Indices: 1068--1128 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
1058 AAAATGGTCA
* *
1068 TTGAGCTATTTAAAA-ATTTTCATTTAAGTTG
1 TTGAACTATTCAAAAGATTTTCATTTAAGTTG
* *
1099 TTGAACTATTCAAAAGTTTTTTATTTAAGT
1 TTGAACTATTCAAAAGATTTTCATTTAAGT
1129 CGATGGGTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 13 0.52
32 12 0.48
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (32 bp):
TTGAACTATTCAAAAGATTTTCATTTAAGTTG
Found at i:4406 original size:22 final size:21
Alignment explanation
Indices: 4380--4420 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
4370 AAATAAATCA
* *
4380 ATAAATATTCAGATGTAACTGG
1 ATAAAGATTAAGATG-AACTGG
4402 ATAAAGATTAAGATGAACT
1 ATAAAGATTAAGATGAACT
4421 TTTCAAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.29
Consensus pattern (21 bp):
ATAAAGATTAAGATGAACTGG
Found at i:4559 original size:3 final size:3
Alignment explanation
Indices: 4553--4580 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4543 ATTCTTACTT
4553 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4581 AACAAAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5552 original size:17 final size:17
Alignment explanation
Indices: 5526--5559 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5516 ATTCTCTAAA
*
5526 TATGTAATATATTTTAT
1 TATGTAATATAATTTAT
*
5543 TATGTTATATAATTTAT
1 TATGTAATATAATTTAT
5560 AACACATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
TATGTAATATAATTTAT
Found at i:9637 original size:3 final size:3
Alignment explanation
Indices: 9629--9735 Score: 58
Period size: 3 Copynumber: 35.7 Consensus size: 3
9619 TAAATGAATC
* * * * * * *
9629 AAT AAT AAT AAT ATT AAT AAT AA- ATAT AAC ACT GAT GAC ATT AATT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AA-T
* * * *
9675 AAT ATT AAT AA- CAT AAC AAT AAT AAT AA- ATAT AAT AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
*
9719 AAT ATT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
9736 CATTTATTTT
Statistics
Matches: 76, Mismatches: 22, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
2 3 0.04
3 68 0.89
4 5 0.07
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:10911 original size:29 final size:29
Alignment explanation
Indices: 10834--10948 Score: 117
Period size: 30 Copynumber: 3.9 Consensus size: 29
10824 CCCTGAAGGT
* *
10834 CCCTAAACTTCTCTAAAATTATATTTTTGA
1 CCCTAAACTT-TCCAAAATTACATTTTTGA
10864 CCCTAAACTTTCCAAAAATTACATTTTT-A
1 CCCTAAACTTTCC-AAAATTACATTTTTGA
*
10893 CCACTAAACTTTCCAAAATTCCA-TTTTGA
1 CC-CTAAACTTTCCAAAATTACATTTTTGA
* **
10922 CCCCAATTTTTCCAAAACTTACCATTT
1 CCCTAAACTTTCCAAAA-TTA-CATTT
10949 ACCCCCGAAC
Statistics
Matches: 72, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
28 16 0.22
29 18 0.25
30 36 0.50
31 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAATTACATTTTTGA
Found at i:11039 original size:30 final size:31
Alignment explanation
Indices: 10848--11046 Score: 117
Period size: 29 Copynumber: 6.8 Consensus size: 31
10838 AAACTTCTCT
* *
10848 AAAATTA-TATTTTTGACCCT-AAACTTTCCA
1 AAAATTACCATTTTT-ACCCTCTAACTTTCCA
*
10878 AAAATTA-CATTTTTACCACT-AAACTTTCC-
1 AAAATTACCATTTTTACC-CTCTAACTTTCCA
* *
10907 AAAATT-CCATTTTGACCC-C-AATTTTTCCA
1 AAAATTACCATTTTTACCCTCTAA-CTTTCCA
* * *
10936 AAACTTACCA--TTTACCCCCGAAC-TTCCA
1 AAAATTACCATTTTTACCCTCTAACTTTCCA
* * *
10964 AAAGTT-CCTTTTTTGA-CCTCT-ATTTTCCAAA
1 AAAATTACCATTTTT-ACCCTCTAACTTTCC--A
10995 AAAATTACCA-TTTTACCCTCTAA-TTTCCA
1 AAAATTACCATTTTTACCCTCTAACTTTCCA
*
11024 AAAATTATCATTTTTACCC-CTAA
1 AAAATTACCATTTTTACCCTCTAA
11047 ACTTCCCTAG
Statistics
Matches: 137, Mismatches: 14, Indels: 37
0.73 0.07 0.20
Matches are distributed among these distances:
27 4 0.03
28 23 0.17
29 48 0.35
30 39 0.28
31 20 0.15
32 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.38
Consensus pattern (31 bp):
AAAATTACCATTTTTACCCTCTAACTTTCCA
Found at i:11110 original size:29 final size:29
Alignment explanation
Indices: 10834--11110 Score: 99
Period size: 30 Copynumber: 9.4 Consensus size: 29
10824 CCCTGAAGGT
* *
10834 CCCTAAACTTCTCTAAAATTA-TATTTTTGA-
1 CCCTAAACTTC-CCAAAATTACCA-TTTT-AC
*
10864 CCCTAAACTTTCCAAAAATTA-CATTTTTAC
1 CCCTAAAC-TTCCCAAAATTACCA-TTTTAC
* *
10894 CACTAAACTTTCCAAAATT-CCATTTTGAC
1 CCCTAAACTTCCCAAAATTACCATTTT-AC
** *
10923 CCC-AATTTTTCCAAAACTTACCA-TTTAC
1 CCCTAAACTTCCCAAAA-TTACCATTTTAC
** *
10951 CCCCGAACTT-CCAAAAGTT-CCTTTTTTGAC
1 CCCTAAACTTCCCAAAA-TTACC-ATTTT-AC
* ** *
10981 CTCT-ATTTTCCAAAAAAATTACCATTTTAC
1 CCCTAAACTTCC--CAAAATTACCATTTTAC
* * *
11011 CCTCT-AATTTCCAAAAATTATCATTTTTAC
1 CC-CTAAACTTCCCAAAATTACCA-TTTTAC
* ** *
11041 CCCTAAACTTCCCTAGCTT-CCATTTTTTAT
1 CCCTAAACTTCCCAAAATTACCA--TTTTAC
* * **
11071 CTCGATTCTTCCCAAAATTACCATTTTAC
1 CCCTAAACTTCCCAAAATTACCATTTTAC
11100 CCCTAAACTTC
1 CCCTAAACTTC
11111 AAAAAATTTC
Statistics
Matches: 187, Mismatches: 41, Indels: 39
0.70 0.15 0.15
Matches are distributed among these distances:
27 2 0.01
28 28 0.15
29 56 0.30
30 75 0.40
31 20 0.11
32 6 0.03
ACGTcount: A:0.31, C:0.29, G:0.03, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTCCCAAAATTACCATTTTAC
Found at i:11124 original size:59 final size:60
Alignment explanation
Indices: 11018--11162 Score: 166
Period size: 59 Copynumber: 2.4 Consensus size: 60
11008 TACCCTCTAA
* *** ** * *
11018 TTTCCAAAAATTATCATTTTTACCCCTAAACTTCCCTAGCTTCCATTTTTTATCTCGATTC
1 TTTCCAAAAATTACCA-TTTTACCCCTAAACTTCAAAAAATTCCATTTTTGATCCCGATTC
* *
11079 -TTCCCAAAATTACCATTTTACCCCTAAACTTCAAAAAATTTCATTTTTGATCCCGATTC
1 TTTCCAAAAATTACCATTTTACCCCTAAACTTCAAAAAATTCCATTTTTGATCCCGATTC
**
11138 TTTATAAAAATTACCATTTTACCCC
1 TTTCCAAAAATTACCATTTTACCCC
11163 CGGATGCCTA
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
59 36 0.51
60 34 0.49
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.41
Consensus pattern (60 bp):
TTTCCAAAAATTACCATTTTACCCCTAAACTTCAAAAAATTCCATTTTTGATCCCGATTC
Found at i:12861 original size:2 final size:2
Alignment explanation
Indices: 12856--12883 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12846 TTTTTTATTA
12856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12884 TTTATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.