Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007844.1 Kokia drynarioides strain JFW-HI SEQ_122481, 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: 39959
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Found at i:3023 original size:7 final size:7
Alignment explanation
Indices: 3011--3038 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3001 AAGATTCTCA
3011 CAACGCC
1 CAACGCC
3018 CAACGCC
1 CAACGCC
3025 CAACGCC
1 CAACGCC
3032 CAACGCC
1 CAACGCC
3039 GTCCATCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.57, G:0.14, T:0.00
Consensus pattern (7 bp):
CAACGCC
Found at i:13614 original size:2 final size:2
Alignment explanation
Indices: 13609--13633 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13599 CAAAAAAGAA
13609 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13634 GGTAAAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18834 original size:17 final size:16
Alignment explanation
Indices: 18814--18859 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
18804 ATATGTCATC
18814 GTAATAATATATTTTTT
1 GTAATAA-ATATTTTTT
*
18831 GTAA-AAAT-TTATTT
1 GTAATAAATATTTTTT
18845 GATAATAAATATTTT
1 G-TAATAAATATTTT
18860 CATTTCAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 6 0.25
15 5 0.21
16 6 0.25
17 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (16 bp):
GTAATAAATATTTTTT
Found at i:22323 original size:30 final size:30
Alignment explanation
Indices: 22289--22383 Score: 145
Period size: 30 Copynumber: 3.2 Consensus size: 30
22279 CAACTTAAAA
*
22289 AACAAATGTCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
*
22319 AACAAATACCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
* * *
22349 AAGAAACGCCTCAAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
22379 AACAA
1 AACAA
22384 TAAAATAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.60, C:0.16, G:0.03, T:0.21
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:22431 original size:14 final size:14
Alignment explanation
Indices: 22408--22442 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
22398 TACAATATCC
*
22408 AAATAATAACAACA
1 AAATAGTAACAACA
22422 AAATAGTAACAACA
1 AAATAGTAACAACA
*
22436 TAATAGT
1 AAATAGT
22443 GAAATTGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:22850 original size:27 final size:28
Alignment explanation
Indices: 22794--22862 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
22784 TTTATCAAAT
*
22794 ATTA-TTTTTTAAAATATCGTAATATCA
1 ATTATTTTTTTAAAATATCATAATATCA
* * *
22821 ATTATTTTTTTAAAAT-TTATATTATTA
1 ATTATTTTTTTAAAATATCATAATATCA
22848 ATTATTATATTTTAA
1 ATTATT-T-TTTTAA
22863 TTCCATAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 17 0.49
28 12 0.34
29 6 0.17
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (28 bp):
ATTATTTTTTTAAAATATCATAATATCA
Found at i:30962 original size:22 final size:20
Alignment explanation
Indices: 30937--30988 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 20
30927 ATACTACTTT
30937 TTATTTTTTTTAAATATTTATA
1 TTATTTTTTTT-AATATTTA-A
**
30959 TTATATTAATTTAATATTTAA
1 TTAT-TTTTTTTAATATTTAA
*
30980 TAATTTTTT
1 TTATTTTTT
30989 ATATTTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
20 3 0.12
21 4 0.17
22 12 0.50
23 5 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTTTTTTAATATTTAA
Found at i:31036 original size:25 final size:25
Alignment explanation
Indices: 31008--31059 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
30998 ATTTATTAAA
* *
31008 ATTTTTATATA-ATCATTTTAATATT
1 ATTTTAATATATA-CATTATAATATT
*
31033 ATTTTAATATTTACATTATAATATT
1 ATTTTAATATATACATTATAATATT
31058 AT
1 AT
31060 ATATTCAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTTTAATATATACATTATAATATT
Found at i:31925 original size:18 final size:19
Alignment explanation
Indices: 31904--31946 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
31894 CAATCAATCA
31904 CAAAT-AATAAAAAGATAT
1 CAAATCAATAAAAAGATAT
*
31922 CAAATTCAATAAAAATATAT
1 CAAA-TCAATAAAAAGATAT
31942 CAAAT
1 CAAAT
31947 TCATAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 2 0.09
20 16 0.73
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (19 bp):
CAAATCAATAAAAAGATAT
Found at i:31932 original size:20 final size:20
Alignment explanation
Indices: 31909--31949 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
31899 AATCACAAAT
31909 AATAAAAAGATATCAAATTC
1 AATAAAAAGATATCAAATTC
*
31929 AATAAAAATATATCAAATTC
1 AATAAAAAGATATCAAATTC
31949 A
1 A
31950 TAACAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (20 bp):
AATAAAAAGATATCAAATTC
Found at i:38910 original size:22 final size:23
Alignment explanation
Indices: 38875--38940 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
38865 CACACACGGT
* *
38875 GCAAATCAGTAGGCACACAAAAT
1 GCAAATAAGTAGGCACACAAAAC
* * *
38898 GC-AATAAGTAGGCGCACATAGC
1 GCAAATAAGTAGGCACACAAAAC
*
38920 GCAAATCAGTAGGCACACAAA
1 GCAAATAAGTAGGCACACAAA
38941 GTGCGAAACA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 17 0.50
23 17 0.50
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (23 bp):
GCAAATAAGTAGGCACACAAAAC
Found at i:38977 original size:23 final size:23
Alignment explanation
Indices: 38830--38979 Score: 110
Period size: 23 Copynumber: 6.4 Consensus size: 23
38820 CGAAGTACTT
* *
38830 AACAGTAAGCACACAAGTGTTGAGGA
1 AACAGTAAGCACACAA-AG-TG-CGA
**
38856 AACAGTAAGCACACACGGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* *
38878 AATCAGTAGGCACACAAAATGC-A
1 AA-CAGTAAGCACACAAAGTGCGA
* * * *
38901 ATA-AGTAGGCGCACATAGCGC-A
1 A-ACAGTAAGCACACAAAGTGCGA
*
38923 AATCAGTAGGCACACAAAGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
*
38947 AACAGTAAGCACACGAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
38970 AACAGTAAGC
1 AACAGTAAGC
38980 GCGCTAGCAT
Statistics
Matches: 103, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.01
22 19 0.18
23 61 0.59
24 6 0.06
25 1 0.01
26 15 0.15
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Done.