Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008619.1 Kokia drynarioides strain JFW-HI SEQ_123298, 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: 13280
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Found at i:506 original size:29 final size:28
Alignment explanation
Indices: 408--661 Score: 156
Period size: 30 Copynumber: 8.6 Consensus size: 28
398 CTGAACTATC
* * *
408 CAAAAATCACGTTTTCACCTCTAAACATTT
1 CAAAAATAACATTTTGACC-CTAAAC-TTT
*
438 CAAAAATTACATTTTGACCCTCAAACTTTT
1 CAAAAATAACATTTTGACCCT-AAAC-TTT
*
468 CAAAAAAAAAAACATTTTGACCCCTAAACTTT
1 C---AAAAATAACATTTTGA-CCCTAAACTTT
*
500 CTAAAAAGT-ACATTTTGACCCTGAAC-TT
1 C-AAAAA-TAACATTTTGACCCTAAACTTT
* * *
528 CACAAAATTACATTTTGACCATGAACTTT
1 CA-AAAATAACATTTTGACCCTAAACTTT
* *
557 CCAAAAATTACCATTTT-ACCCCTAAACTTC
1 -CAAAAA-TAACATTTTGA-CCCTAAACTTT
* * * *
587 CAAAAATCACATTTTTG-CCCTCGAACATC
1 CAAAAATAACA-TTTTGACCCT-AAACTTT
*
616 CAAAAATTACCATTTTGACCCTAAACTTTT
1 CAAAAA-TAACATTTTGACCCTAAAC-TTT
* *
646 CAAAATTACCATTTTG
1 CAAAAATAACATTTTG
662 CCCCCGAGCA
Statistics
Matches: 181, Mismatches: 25, Indels: 37
0.74 0.10 0.15
Matches are distributed among these distances:
27 2 0.01
28 30 0.17
29 55 0.30
30 68 0.38
32 4 0.02
33 18 0.10
34 4 0.02
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.32
Consensus pattern (28 bp):
CAAAAATAACATTTTGACCCTAAACTTT
Found at i:572 original size:58 final size:56
Alignment explanation
Indices: 479--745 Score: 220
Period size: 58 Copynumber: 4.6 Consensus size: 56
469 AAAAAAAAAA
* * * * *
479 ACATTTTGACCCCTAAACTTTCTAAAAAGTA-CATTTTGACCCTGAACTTCACAAAATT
1 ACATTTTGA-CCCTGAAC-ATCCAAAAATTACCATTTTGACCCTAAACTTC-CAAAATT
* * *
537 ACATTTTGACCATGAACTTTCCAAAAATTACCATTTT-ACCCCTAAACTTCCAAAAATC
1 ACATTTTGACCCTGAAC-ATCCAAAAATTACCATTTTGA-CCCTAAACTTCC-AAAATT
*
595 ACATTTTTG-CCCTCGAACATCCAAAAATTACCATTTTGACCCTAAACTTTTCAAAATT
1 ACA-TTTTGACCCT-GAACATCCAAAAATTACCATTTTGACCCTAAAC-TTCCAAAATT
* * * * * *
653 ACCATTTTGCCCCCGAGCATCCAAAAATTACCATTTTG-CCCCAATCATCCAAAAATT
1 A-CATTTTGACCCTGAACATCCAAAAATTACCATTTTGACCCTAAACTTCC-AAAATT
* * *
710 ATCATTTTGCCCCT-AAGTATCCAAAAAGTACCATTT
1 A-CATTTTGACCCTGAA-CATCCAAAAATTACCATTT
746 CACCCTCAAA
Statistics
Matches: 177, Mismatches: 21, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
56 3 0.02
57 60 0.34
58 96 0.54
59 18 0.10
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.31
Consensus pattern (56 bp):
ACATTTTGACCCTGAACATCCAAAAATTACCATTTTGACCCTAAACTTCCAAAATT
Found at i:679 original size:29 final size:29
Alignment explanation
Indices: 556--745 Score: 179
Period size: 29 Copynumber: 6.6 Consensus size: 29
546 CCATGAACTT
* * *
556 TCCAAAAATTACCATTTTACCCCTAAACT
1 TCCAAAAATTACCATTTTGCCCCCAAACA
* * *
585 TCCAAAAATCA-CATTTTTGCCCTCGAACA
1 TCCAAAAATTACCA-TTTTGCCCCCAAACA
* * *
614 TCCAAAAATTACCATTTTGACCCTAAACTT
1 TCCAAAAATTACCATTTTGCCCCCAAAC-A
* * *
644 TTC-AAAATTACCATTTTGCCCCCGAGCA
1 TCCAAAAATTACCATTTTGCCCCCAAACA
*
672 TCCAAAAATTACCATTTTG-CCCCAATCA
1 TCCAAAAATTACCATTTTGCCCCCAAACA
* * **
700 TCCAAAAATTATCATTTTGCCCCTAAGTA
1 TCCAAAAATTACCATTTTGCCCCCAAACA
*
729 TCCAAAAAGTACCATTT
1 TCCAAAAATTACCATTT
746 CACCCTCAAA
Statistics
Matches: 129, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
28 29 0.22
29 96 0.74
30 4 0.03
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTGCCCCCAAACA
Found at i:3761 original size:18 final size:18
Alignment explanation
Indices: 3738--3774 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3728 ACAATACCAA
3738 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
3756 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
3774 T
1 T
3775 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:4105 original size:17 final size:18
Alignment explanation
Indices: 4073--4106 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4063 AATTTATATC
4073 CAATTTATACCCTAATTT
1 CAATTTATACCCTAATTT
*
4091 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
4107 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (18 bp):
CAATTTATACCCTAATTT
Found at i:6878 original size:27 final size:27
Alignment explanation
Indices: 6828--6879 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
6818 GTGCATATGC
* *
6828 CGTCGATACAGTAAATCGCCATATTAT
1 CGTCGATACAGTAAATCACAATATTAT
*
6855 CGTCGATGCAGTAAATCACAATATT
1 CGTCGATACAGTAAATCACAATATT
6880 TCAATCAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (27 bp):
CGTCGATACAGTAAATCACAATATTAT
Found at i:7299 original size:32 final size:31
Alignment explanation
Indices: 7258--7320 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
7248 AAGGGTTTGA
7258 GGGGGTTGGGAAGAGAAGGAAAGTAAAAGAGT
1 GGGGGTTGGGAAGAGAAGGAAAGT-AAAGAGT
* *
7290 GGGGGTTGGGAGGAGAAGGGAAGTAAAGAGT
1 GGGGGTTGGGAAGAGAAGGAAAGTAAAGAGT
7321 TTGGTATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.13
Consensus pattern (31 bp):
GGGGGTTGGGAAGAGAAGGAAAGTAAAGAGT
Found at i:7778 original size:24 final size:24
Alignment explanation
Indices: 7744--7803 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
7734 TTACAAGGAC
* *
7744 ATGAAAGGTGAAGGGTTAAGGAAG
1 ATGAAAGGTGAAGAGTTAAGAAAG
*
7768 ATGAAATGTGAAGAGTTAAGAAAG
1 ATGAAAGGTGAAGAGTTAAGAAAG
7792 ATGAAAGGTGAA
1 ATGAAAGGTGAA
7804 AGATTGAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.35, T:0.18
Consensus pattern (24 bp):
ATGAAAGGTGAAGAGTTAAGAAAG
Found at i:11067 original size:18 final size:18
Alignment explanation
Indices: 11044--11086 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
11034 ATCTGATGAA
11044 AAAACATGTAATCTTTCC
1 AAAACATGTAATCTTTCC
*
11062 AAAACATGTAGTCTTTCC
1 AAAACATGTAATCTTTCC
11080 AAAACAT
1 AAAACAT
11087 ATTTCTTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (18 bp):
AAAACATGTAATCTTTCC
Found at i:11095 original size:17 final size:18
Alignment explanation
Indices: 11044--11097 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
11034 ATCTGATGAA
* *
11044 AAAACATGTAATCTTTCC
1 AAAACATATAGTCTTTCC
*
11062 AAAACATGTAGTCTTTCC
1 AAAACATATAGTCTTTCC
*
11080 AAAACATAT-TTCTTTCC
1 AAAACATATAGTCTTTCC
11097 A
1 A
11098 CTTTCAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 8 0.24
18 25 0.76
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (18 bp):
AAAACATATAGTCTTTCC
Done.