Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002827.1 Kokia drynarioides strain JFW-HI SEQ_115186, 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: 4078
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Found at i:217 original size:24 final size:24
Alignment explanation
Indices: 190--240 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
180 ATTTTGACTC
* * * *
190 AAACAACTAAATAGAGTTTAATTG
1 AAACAAATAAATAAAATTTAACTG
214 AAACAAATAAATAAAATTTAACTG
1 AAACAAATAAATAAAATTTAACTG
238 AAA
1 AAA
241 GATTATTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.25
Consensus pattern (24 bp):
AAACAAATAAATAAAATTTAACTG
Found at i:1813 original size:13 final size:13
Alignment explanation
Indices: 1795--1830 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
1785 AGAAATTGAG
1795 AAATTTAACGCAC
1 AAATTTAACGCAC
1808 AAATTTAACGCAC
1 AAATTTAACGCAC
1821 AAATTTAACG
1 AAATTTAACG
1831 TAAAAAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.47, C:0.19, G:0.08, T:0.25
Consensus pattern (13 bp):
AAATTTAACGCAC
Found at i:2808 original size:6 final size:6
Alignment explanation
Indices: 2797--2880 Score: 65
Period size: 6 Copynumber: 14.7 Consensus size: 6
2787 CTGGGCCCAA
* * *
2797 TAAATT TAAATT T-ATTT TAAAAT TAAGTT T--ATT CTAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT
2843 T--ATT TAAAATT TAAATT T--ATT ATAAATT TAAATT TAAA
1 TAAATT T-AAATT TAAATT TAAATT -TAAATT TAAATT TAAA
2881 ATCTATTTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
4 9 0.15
5 6 0.10
6 37 0.60
7 10 0.16
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:2822 original size:17 final size:17
Alignment explanation
Indices: 2797--2878 Score: 119
Period size: 17 Copynumber: 4.8 Consensus size: 17
2787 CTGGGCCCAA
2797 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* * *
2814 TAAAATTAAGTTTATTC
1 TAAATTTAAATTTATTT
2831 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* *
2848 AAAATTTAAATTTATTA
1 TAAATTTAAATTTATTT
2865 TAAATTTAAATTTA
1 TAAATTTAAATTTA
2879 AAATCTATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:2840 original size:34 final size:34
Alignment explanation
Indices: 2796--2878 Score: 132
Period size: 34 Copynumber: 2.4 Consensus size: 34
2786 TCTGGGCCCA
*
2796 ATAAATTTAAATTTATTTTAAAA-TTAAGTTTATT
1 ATAAATTTAAATTTA-TTTAAAATTTAAATTTATT
*
2830 CTAAATTTAAATTTATTTAAAATTTAAATTTATT
1 ATAAATTTAAATTTATTTAAAATTTAAATTTATT
2864 ATAAATTTAAATTTA
1 ATAAATTTAAATTTA
2879 AAATCTATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 7 0.16
34 38 0.84
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (34 bp):
ATAAATTTAAATTTATTTAAAATTTAAATTTATT
Found at i:2852 original size:11 final size:10
Alignment explanation
Indices: 2834--2892 Score: 52
Period size: 10 Copynumber: 5.8 Consensus size: 10
2824 TTTATTCTAA
2834 ATTTAAATTT
1 ATTTAAATTT
2844 ATTTAAA---
1 ATTTAAATTT
2851 ATTTAAATTT
1 ATTTAAATTT
2861 ATTATAAATTT
1 ATT-TAAATTT
*
2872 AAATTTAAAATCT
1 --ATTT-AAATTT
2885 ATTTAAAT
1 ATTTAAAT
2893 AATATACAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
7 7 0.17
10 14 0.34
11 11 0.27
12 1 0.02
13 8 0.20
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:2882 original size:24 final size:23
Alignment explanation
Indices: 2844--2892 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
2834 ATTTAAATTT
*
2844 ATTTAAAATTTAAATTTATTATAA
1 ATTTAAAATTTAAATCTATT-TAA
2868 ATTT-AAATTTAAAATCTATTTAA
1 ATTTAAAATTT-AAATCTATTTAA
2891 AT
1 AT
2893 AATATACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTAAAATTTAAATCTATTTAA
Found at i:3586 original size:3 final size:3
Alignment explanation
Indices: 3578--3648 Score: 79
Period size: 3 Copynumber: 23.0 Consensus size: 3
3568 AATAAGGTTT
** **
3578 TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TTG TTT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
*
3624 TAA TAA TAT TAA TTAA TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA
3649 AAAAGAAACG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
3 53 0.90
4 6 0.10
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:3616 original size:37 final size:37
Alignment explanation
Indices: 3574--3646 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
3564 AACAAATAAG
3574 GTTTTAATAATAATAATAATAATAA-TAATAAATAATT
1 GTTTTAATAATAATAATAATAATAATTAAT-AATAATT
*
3611 GTTTTAATAATAATAATAATATTAATTAATAATAAT
1 GTTTTAATAATAATAATAATAATAATTAATAATAAT
3647 AAAAAAGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 30 0.88
38 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (37 bp):
GTTTTAATAATAATAATAATAATAATTAATAATAATT
Done.