Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006019.1 Kokia drynarioides strain JFW-HI SEQ_120462, 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: 3739
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.34
Found at i:2656 original size:15 final size:15
Alignment explanation
Indices: 2636--2739 Score: 102
Period size: 15 Copynumber: 6.9 Consensus size: 15
2626 CATTTATGTT
2636 CAGCATTTGGTACCG
1 CAGCATTTGGTACCG
*
2651 CAGCATTTGGTACCC
1 CAGCATTTGGTACCG
* **
2666 CAGCATTCGGTATAG
1 CAGCATTTGGTACCG
2681 CAGCATTTGGTA-CG
1 CAGCATTTGGTACCG
* **
2695 ACAACATTTGGTACAA
1 -CAGCATTTGGTACCG
* * *
2711 CCGCATTTGGTATCA
1 CAGCATTTGGTACCG
2726 CAGCATTTGGTACC
1 CAGCATTTGGTACC
2740 CCTACATTTG
Statistics
Matches: 71, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
14 1 0.01
15 70 0.99
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (15 bp):
CAGCATTTGGTACCG
Found at i:2670 original size:30 final size:30
Alignment explanation
Indices: 2636--2738 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
2626 CATTTATGTT
* *
2636 CAGCATTTGGTACCGCAGCATTTGGTACCC
1 CAGCATTTGGTACAGCAGCATTTGGTACCA
* * *
2666 CAGCATTCGGTATAGCAGCATTTGGTACGA
1 CAGCATTTGGTACAGCAGCATTTGGTACCA
* * * *
2696 CAACATTTGGTACAACCGCATTTGGTATCA
1 CAGCATTTGGTACAGCAGCATTTGGTACCA
2726 CAGCATTTGGTAC
1 CAGCATTTGGTAC
2739 CCCTACATTT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (30 bp):
CAGCATTTGGTACAGCAGCATTTGGTACCA
Found at i:2703 original size:45 final size:44
Alignment explanation
Indices: 2636--2738 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 44
2626 CATTTATGTT
* *
2636 CAGCATTTGGTACCGCAGCATTTGGTAC-CCCAGCATTCGGTAT-A
1 CAGCATTTGGTA-CGCAACATTTGGTACAACC-GCATTCGGTATCA
*
2680 GCAGCATTTGGTACGACAACATTTGGTACAACCGCATTTGGTATCA
1 -CAGCATTTGGTACG-CAACATTTGGTACAACCGCATTCGGTATCA
2726 CAGCATTTGGTAC
1 CAGCATTTGGTAC
2739 CCCTACATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
44 2 0.04
45 47 0.90
46 3 0.06
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (44 bp):
CAGCATTTGGTACGCAACATTTGGTACAACCGCATTCGGTATCA
Found at i:2747 original size:45 final size:44
Alignment explanation
Indices: 2636--2750 Score: 126
Period size: 45 Copynumber: 2.5 Consensus size: 44
2626 CATTTATGTT
* *
2636 CAGCATTTGGTACCGCAGCATTTGGTACCCCAGCATTCGGTATAG
1 CAGCATTTGGTACCACA-CATTTGGTACACCAGCATTCGGTATAG
* *
2681 CAGCATTTGGTACGACAACATTTGGTACAACC-GCATTTGGTATCA-
1 CAGCATTTGGTACCAC-ACATTTGGTAC-ACCAGCATTCGGTAT-AG
*
2726 CAGCATTTGGTACCCCTACATTTGG
1 CAGCATTTGGTACCAC-ACATTTGG
2751 CATAGCAGCA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
45 56 0.93
46 4 0.07
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (44 bp):
CAGCATTTGGTACCACACATTTGGTACACCAGCATTCGGTATAG
Found at i:2748 original size:30 final size:30
Alignment explanation
Indices: 2636--2769 Score: 107
Period size: 30 Copynumber: 4.5 Consensus size: 30
2626 CATTTATGTT
* *
2636 CAGCATTTGGTAC-CGCAGCATTTGGTACCC
1 CAGCATTTGGTACAC-CAGCATTTGGTATCA
* * *
2666 CAGCATTCGGTATAGCAGCATTTGGTA-CGA
1 CAGCATTTGGTACACCAGCATTTGGTATC-A
*
2696 CAACATTTGGTACAACC-GCATTTGGTATCA
1 CAGCATTTGGTAC-ACCAGCATTTGGTATCA
* *
2726 CAGCATTTGGTACCCCTA-CATTTGGCAT-A
1 CAGCATTTGGTACACC-AGCATTTGGTATCA
*
2755 GCAGCAATTGGTACA
1 -CAGCATTTGGTACA
2770 TCGGCATAGG
Statistics
Matches: 84, Mismatches: 13, Indels: 14
0.76 0.12 0.13
Matches are distributed among these distances:
29 4 0.05
30 77 0.92
31 3 0.04
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.28
Consensus pattern (30 bp):
CAGCATTTGGTACACCAGCATTTGGTATCA
Found at i:2766 original size:45 final size:45
Alignment explanation
Indices: 2636--2767 Score: 115
Period size: 45 Copynumber: 2.9 Consensus size: 45
2626 CATTTATGTT
* * * **
2636 CAGCATTTGGTACCGCAGCATTTGGTACCCCAGC-ATTCGGTAT-A
1 CAGCATTTGGTACCACAACATTTGGCACAACAGCAATT-GGTATCA
* * * *
2680 GCAGCATTTGGTACGACAACATTTGGTACAACCGCATTTGGTATCA
1 -CAGCATTTGGTACCACAACATTTGGCACAACAGCAATTGGTATCA
* * * *
2726 CAGCATTTGGTACCCCTACATTTGGCATAGCAGCAATTGGTA
1 CAGCATTTGGTACCACAACATTTGGCACAACAGCAATTGGTA
2768 CATCGGCATA
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
45 67 0.96
46 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (45 bp):
CAGCATTTGGTACCACAACATTTGGCACAACAGCAATTGGTATCA
Done.